This excerpt is taken from the 5th Edition of the Confessional Presbyterian.
“The third opinion [of liberty of conscience] is that the Magistrate may and ought to exercise his coercive power, in suppressing and punishing heretics and sectaries, less or more, according as the nature and degree of the error, schism, obstinacy, and danger of seducing others, requires. This as it was the judgment of the orthodox ancients (vide Optati opera, edit. Al Baspin, p. 204, 215), so it is followed by our soundest Protestant writers; most largely by Beza against Bellius and Monfortius, in a particular treatise, De Haereticis a Magistratu Puniendis. And though Gerhard, Brochmand, and other Lutheran writer, make a controversy where they need not, alleging that the Calvinists (so nicknamed) hold as the Papists do, that all heretics without distinction are to be put to death: the truth is, they themselves say as much as either Calvin or Beza, or any other whom they take for adversaries in this question, that is, that heretics are to be punished by mulcts [fines], imprisonments, banishments, and if they be gross idolaters or blasphemers, and seducers of others, then to be put to death. What is it else that Calvin teaches, when he distinguishes three kinds of errors: some to be tolerated with a spirit of meekness, and such as ought not to separate brethren; others not to be tolerated, but to be suppressed with a certain degree of severity; a third sort so abominable and pestiferous, that they are to be cut off by the highest punishment?
And lest it be thought that this is but the opinion of some few, that the magistrate ought thus by a strong hand, and by civil punishments suppress heretics and sectaries: let it be observed what is held forth and professed concerning this business, by the Reformed Churches in their public confessions of faith…
II. The arguments whereby this third or middle opinion is confirmed (that we may not build upon human authority) are these.
1. First, the law (Deut. 13:6-9), concerning the stoning and killing of him, who shall secretly entice people, saying, “Let us go after other gods.” If it said, that this law did bind the Jew only, and is not moral or perpetual, I answer, Jacobus Acontius, though he is of another opinion concerning this question than I am, yet he candidly and freely confesses that he sees nothing in that law which does not belong to the New Testament, as well as the Old; for, he says, the reason and ground of the law, the use and end of it, is moral and perpetual (v. 11): All Israel shall here and fear, and shall do no more any such wickedness, as this is among you. But yet, says Acontius, this law does not concern heretics, who believe and teach errors concerning the true God or his worship; but only apostates who fall away to other gods. In this I shall not much contend with him; only thus far, if apostates are to be stoned and killed according to the law then surely seducing heretics are also to receive their measure and proportion of punishment. The moral equity of the law requires this much at least, that is we compare heresy and apostasy together, look how much less the evil of sin is in heresy, so much and no more is to be remitted of the evil of punishment, especially the danger of contagion and seduction, being as much of rather more in heresy then in apostasy; yea, that which is called heresy being oftentimes a real following after other gods. But the Law (Deut. 13), for punishing with death, as well whole cities as particular persons, for falling away to other gods, is not the only law for punishing even capitally gross sins against the first table. See EX. 22:20, He that sacrifieth unto any god, save unto the Lord only, he shall be utterly destroyed. Ex. 31:14, Every one that defileth the sabbath, shall be put to death. Lev. 24:16, And he that blasphemeth the name of the Lord, he shall surely be put to death. Deut. 17:2-5, If there be found among you within any of thy gates, which the Lord thy God giveth thee, man and woman, that hath wrought wickedness in the sight of the Lord they God, in transgressing his covenant, and hath gone and served other gods and worshipped them… Thou shalt bring forth that man or that woman unto thy gates, even that man or that woman, and shall stone them with stones till they die.
It will be asked, “But how does it appear that these or any other judicial laws of Moses do at all appertain to us, as rules to guide us in like cases?” I shall wish him who scruples this, to read Piscator’s appendix to his observations upon the 21-23 chapters of Exodus, where he excellently disputes this question, whether the Christian Magistrate is bound to observe the judicial laws of Moses, as well as the Jewish Magistrate was. He answers by the common distinction, he is obliged to those things in the judicial law which are unchangeable, and common to all nations: but not to those things which are mutable, or proper to the Jewish Republic. But then he explains this distinction, that by things mutable, and proper to the Jews, he understands the emancipation of an Hebrew servant or handmaid in the seventh year, a man’s marrying his brother’s wife and raising up seed to his brother, the forgiving of debts at the Jubilee, marrying with one of the same tribe, and if there be any other like to these; also ceremonial trespasses, as touching a dead body, etc. But things immutable, and common to all nations, are the laws concerning moral trespass, sins against the moral law, as murder, adultery, theft, enticing away from God, blasphemy, striking of parents. Now that the Christian magistrate is bound to observe these judicial laws of Moses, which appoint the punishments of sins against the moral law, he proves by these reasons.
(1.) If it were not so, then is it free and arbitrary to the Magistrate to appoint what punishments he pleases. But this is not arbitrary to him, for he is the minister of God, (Rom. 13:4) and the judgment is the Lord’s (Deut. 1:7; 2 Chron. 19:6). And if the Magistrate is keeper of both tables, he must keep them in such manner as God has delivered them to him.
(2.) Christ’s words (Matt 5:17), Think not that I am come to destroy the Law or the Prophets, I am not come to destroy, but to fulfill, are comprehensive of the judicial law, it being a part of the law of Moses. Now he could not fulfill the judicial law, except either by his practice, of by teaching others still to observe it; not by his own practice, for he would not condemn the adulteress (Jn. 8:11), nor divide the inheritance (Luke 12:13-14). Therefore it must be by his doctrine for our observing it.
(3.) If Christ in his sermon (Matt. 5), would teach that the moral law belongs to us Christians, in so much as he vindicates it from false glosses of the scribes and Pharisees; then he meant to hold forth the judicial law concerning moral trespasses as belonging unto us also; for he vindicates and interprets the judicial law, as well as the moral (Matt. 5:38), An eye for an eye, etc.
(4.) If God would have the moral law transmitted from the Jewish people to the Christian people; then he would also have the judicial laws transmitted from the Jewish Magistrate to the Christian Magistrate: there being the same reason of immutability in the punishments, which is in the offenses. Idolatry and adultery displease God now as much as then; and theft displeases God now no more than before.
(5.) Whatsoever things were written aforetime, were written for our learning (Rom. 15:4), and what shall the Christian Magistrate learn more from those judicial laws, but the will of God to be his rule in like cases? The ceremonial law was written for our learning, that we might know the fulfilling of all those types, but the judicial law was not typical.
(6.) Do all to the glory of God (1 Cor. 10:31; Matt. 5:16). How shall Christian Magistrates glorify God more than by observing God’s own laws, as most just, and such as they cannot make better?
(7.) Whatsoever is not of faith is sin (Rom. 14:23). Now when the Christian Magistrate punishes sins against the moral law, if he does this in faith and in assurance of pleasing God, he must have his assurance from the Word of God, for faith can build upon no other foundation; it is the Word which must assure the conscience: God has commanded such a thing, therefore it is my duty to do it; God has forbidden such a thing; therefore I am free to do it. But the will of God concerning civil justice and punishments is no where so fully and clearly revealed as in the judicial law of Moses. This therefore must be the surest prop and stay to the conscience of the Christian Magistrate.
These are not my reasons (if it be not a word or two added by way of explaining and strengthening), but the substance of Piscator’s reasons. Unto which I add, 1. Though we have clear and full scriptures in the New Testament for abolishing the ceremonial law, yet we no where read in all the New Testament of the abolishing of the judicial law, so far as it did concern the punishing of sins against the moral law, of which heresy and seducing of souls is one, and a great one. Once God did reveal his will for punishing those sins by such and such punishments. He who will hold that the Christian Magistrate is not bound to inflict such punishments for such sins, is bound to prove that those former laws of God are abolished, and to show some scriptures for it.
2. That judicial law for having two or three witnesses in judgment (Deut. 19:15; Heb. 10:28), is transferred even with an obligation to us Christians, and it concerns all judgment, as well ecclesiastical as civil (Matt. 18:16; 2 Cor. 13:1), and some other particulars might be instanced, in which are pressed and enforced from the judicial law, by some who yet mind not the obligation of it. To conclude therefore this point, though other judicial or forensical laws concerning the punishments of sins against the moral law may, yea, must be allowed of in Christian Republics and Kingdoms; provided always, they are not contrary or contradictory to God’s own judicial laws; yet I fear not to hold with Junius, De Politiae Mosis, that he who was punishable by death under the judicial law, is punishable by death still; and he who was not punished by death then, is not to be punished by death now. And so much for the first argument from the Law of God…
IV. But now after all this debate upon the question in hand, and after all these arguments for the affirmative and for the negative, some will happily desire and expect some further modification and explanation of the matter in certain positive conclusions or distinguishing assertions. For those whose satisfaction I say, First, there are five sorts of toleration proceeding from five different principles. 1. Of indifferency. 2. Of policy. 3. Of pretended conscience and equity. 4. Of necessity. 5. Of charity…
The fifth and last is that kind of toleration whereby the Magistrate when it is in the power of his hand to punish and extirpate, yet having to do with such of whom there is good hope either of reducing them by convincing their judgments, or of uniting them to the Church by a safe accommodation of differences, he grants them a supersedeas [forbearance]; or though there be no such ground of hope concerning them, yet while he might crush them with the foot of power, in Christian piety and moderation, he forbears so far as may not be destructive to the peace and right government of the Church, using his coercive power with such a mixture of mercy as creates no mischief to the rest of the Church. I speak not only of bearing with those who are weak in faith (Rom. 15:1), but of sparing even those who have perverted the faith, so far as the word of God and rules of Christian moderation would have severity tempered with mercy: that is (as has been said) so far as is not destructive to the Church’s peace, nor shakes the foundations of the established form of church government, and no further; these last two kinds of toleration are allowed; the first three are wholly condemned.
My second distinction is concerning the punishments inflicted by the Magistrate upon heretics. They are either exterminative, or medicinal. Such as blaspheme God or Jesus Christ, or who shall fall away themselves and seduce others to idolatry, ought to be utterly cut off according to the law of God. But as for other heretics, they are to be chastened with medicinal punishments as mulcts [fines; forfeiture], imprisonments, banishments, by which, through God’s blessing, they may be humbled, ashamed, and reduced. Not that I think the proper end of civil and coercive punishments to be the conversion and salvation of the delinquent (which is the end of the church censures and of excommunication itself), but that the right method of proceeding does require that the Magistrate inflict the smaller punishments first, that there may be place for the offenders bringing forth of fruits worthy of repentance, and he may be at least reduced to external order and obedience, being persuaded by the terror of civil power, which may and does (when blessed of God) prove a preparation to free obedience, as the needle is to the thread, or the law to the gospel, servile fear to filial fear; and that the Magistrate step not up to the highest justice till other punishments have proved ineffectual: which made Constantine punish the heretics of his time not with death, but with banishment, as is manifest by the Proem of the Council of Nicea. In such cases it may be said to the heretic of the Magistrate, He is the minster of God to thee for good, more good I am sure, than if the golden reins of civil justice should be loosed, and he suffered to do what he list [likes]. Therefore Augustine likens this coercive punishing of heretics to Sarah’s dealing roughly with Hagar, for her good and humiliation. I conclude, convenience and indulgence to heretics is a cruel mercy: correction is a merciful severity, and a wholesome medicine, as well to themselves as to the Church.”
[Anonymous], George Gillespie, Wholesome Severity Reconciled with Christian Liberty (1645) Wing g765; new edition printed in An Anthology of Presbyterian & Reformed Literature 4 (Dallas, Tex: Naphtali Press, 1991) 181-183; 193-195. Cited from The Anonymous Writings of George Gillespie (Naphtali Press, 2008) 52-58; 76; 78-79.