Pretended Liberty of Conscience
The Toleration of Heresy & Blasphemy
Westminster Confession of Faith 
Chapter XX. Of Christian Liberty, and Liberty of Conscience.III. They who, upon pretence of Christian liberty, do practice any sin, or cherish any lust, do thereby destroy the end of Christian liberty, which is, that being delivered out of the hands of our enemies, we might serve the Lord, without fear, in holiness and righteousness before Him, all the days of our life[o].Chapter XXIII. Of the Civil Magistrate.
(o) Gal. 5:13; I Pet. 2:16; II Pet. 2:19; John 8:34; Luke 1:74, 75.
IV. And because the powers which God hath ordained, and the liberty which Christ hath purchased, are not intended by God to destroy, but mutually to uphold and preserve one another; they who, upon pretence of Christian liberty, shall oppose any lawful power, or the lawful exercise of it, whether it be civil or ecclesiastical, resist the ordinance of God[p]. And, for their publishing of such opinions, or maintaining of such practices, as are contrary to the light of nature, or to the known principles of Christianity, whether concerning faith, worship, or conversation; or, to the power of godliness; or, such erroneous opinions or practices, as either in their own nature, or in the manner of publishing or maintaining them, are destructive to the external peace and order which Christ hath established in the Church, they may lawfully be called to account, and proceeded against by the censures of the Church[q], and by the power of the civil magistrate[r].
(p) Matt. 12:25; I Pet. 2:13, 14, 16; Rom. 13:1 to 8; Heb. 13:17.
(q) Rom. 1:32 with I Cor. 5:1, 5, 11, 13; II John ver. 10, 11, and II Thess. 3:14, and I Tim. 6:3, 4, 5, and Tit. 1:10, 11, 13, and Tit. 3:10 with Matt. 18:15, 16, 17; I Tim. 1:19, 20; Rev. 2:2, 14, 15, 20; Rev. 3:9.
(r) Deut. 13:6 to 12; Rom. 13:3, 4 with II John ver. 10, 11; Ezra 7:23, 25, 26, 27, 28; Rev. 17:12, 16, 17; Neh. 13:15, 17, 21, 22, 25, 30; II Kings 23:5, 6, 9, 20, 21; II Chron. 34:33; II Chron. 15:12, 13, 16; Dan. 3:29; I Tim. 2:2; Isa. 49:23; Zech. 13:2, 3.III. The civil magistrate may not assume to himself the administration of the Word and sacraments, or the power of the keys of the kingdom of heaven[e]: yet he hath authority, and it is his duty, to take order, that unity and peace be preserved in the Church, that the truth of God be kept pure and entire; that all blasphemies and heresies be suppressed; all corruptions and abuses in worship and discipline prevented or reformed; and all the ordinances of God duly settled, administrated, and observed[f]. For the better effecting whereof, he hath power to call synods, to be present at them, and to provide that whatsoever is transacted in them be according to the mind of God[g].Chapter XXXI. Of Synods and Councils.
(e) II Chron. 26:18 with Matt. 18:17 and Matt. 16:19; I Cor. 12:28, 29; Eph. 4:11, 12; I Cor. 4:1, 2; Rom. 10:15; Heb. 5:4.
(f) Isa. 49:23; Ps. 122:9; Ezra 7:23, 25, 26, 27, 28; Lev. 24:16; Deut. 13:5, 6, 12; I Kings 18:4; I Chron. 13:1 to 9; II Kings 23:1 to 26; II Chron. 34:33; II Chron. 15:12, 13.
(g) II Chron. 19:8, 9, 10, 11; II Chron. 29 and 30; Matt. 2:4, 5.II. As magistrates may lawfully call a synod of ministers, and other fit persons, to consult and advise with, about matters of religion[b]; so, if magistrates be open enemies to the Church, the ministers of Christ of themselves, by virtue of their office, or they, with other fit persons upon delegation from their Churches, may meet together in such assemblies[c].1
(b) Isa. 49:23; I Tim. 2:1, 2; II Chron. 19:8, 9, 10, 11; II Chron. 29, 30 chaps.; Matt. 2:4, 5; Prov. 11:14.
(c) Acts 15:2, 4, 22, 23, 25.
Westminster Larger Catechism 
Question 109: What are the sins forbidden in the second commandment?
Answer: The sins forbidden in the second commandment are, all devising, counseling, commanding, using, and anywise approving, any religious worship not instituted by God himself; tolerating a false religion; the making any representation of God, of all or of any of the three persons, either inwardly in our mind, or outwardly in any kind of image or likeness of any creature: Whatsoever; all worshiping of it, or God in it or by it; the making of any representation of feigned deities, and all worship of them, or service belonging to them; all superstitious devices, corrupting the worship of God, adding to it, or taking from it, whether invented and taken up of ourselves, or received by tradition from others, though under the title of antiquity, custom, devotion, good intent, or any other pretense: Whatsoever; simony; sacrilege; all neglect, contempt, hindering, and opposing the worship and ordinances which God has appointed.
1. On this point, one might note the following, excerpted from:
Assembly at EDINBURGH, August 27, 1647. Sess. 23.
Act approving the CONFESSION of FAITH.
It is further declared, That the Assembly understandeth some parts of the second article of the thirty-one chapter only of kirks not settled, or constituted in point of government: And that although, in such kirks, a synod of Ministers, and other fit persons, may be called by the Magistrate's authority and nomination, without any other call, to consult and advise with about matters of religion; and although, likewise, the Ministers of Christ, without delegation from their churches, may of themselves, and by virtue of their office meet together synodically in such kirks not yet constituted, yet neither of these ought to be done in kirks constituted and settled; it being always free to the Magistrate to advise with synods of Ministers and Ruling Elders, meeting upon delegation from their churches, either ordinarily, or, being indicted by his authority, occasionally, and pro re nata; it being also free to assemble together synodically, as well pro re nata as at the ordinary times, upon delegation from the churches, by the intrinsical power received from Christ, as often as it is necessary for the good of the Church so to assemble, in case the Magistrate, to the detriment of the Church, withhold or deny his consent; the necessity of occasional assemblies being first remonstrate unto him by humble supplication.