Historically most Reformed confessions have reflected a view of civil government that included the "establishment principle". They taught that the civil magistrate was authorized, empowered, and commanded to establish and support the true church and to suppress all false and heretical churches and sects. Historically Presbyterians in the United States have rejected this view, particularly as contained in Chapter 23 of the original Westminster Confession of Faith. In 1729, in the Adopting Act, when the newly organized Presbyterian Church in the USA adopted the Westminster standards as her own, they took exception to chapter 23 and its doctrine of the civil magistrate. The American Presbyterian Church continues in that tradition.
The American Presbyterian Church confesses that civil government is an institution of God established by God in his covenant with the patriarch Noah. Before that God had forbidden anyone to exact vengeance for sin in his name and had warned men not to take the law in their own hands in dealing with Cain, the first murderer. However now God commanded Noah that , "Whoso sheddeth man’s blood, by man shall his blood be shed: for in the image of God made he man" (Genesis 9:6). This authorized man, through the agency of civil government, to punish sin in God’s stead. The particular sin that men were called to punish was murder, not a violation of matters of faith or worship.
The American Presbyterian Church however rejects the notion that civil government ought to be secular or that it is some kind of social compact. With the Apostle Paul we affirm that civil magistrates are ministers of God. However we believe that God has limited their authority to enforcing the second table of the law. These are the very commandments that Paul quotes in his famous passage on civil government in Romans 13. We believe that civil government is an earthly ministry of justice established by God to restrain sin and to punish sins that men commit in their relationships to each other as regulated by the second table of the law. Similarly we believe that God has established the church, and raised up ecclesiastical elders, to enforce the first table of the law, and to discipline men in matters of faith and worship. We therefore believe in two divine institutions, with two separate sets of elders, enforcing respectively two different tables of the law.
This is the historic position of American Presbyterianism and we believe that it is also the scriptural position. The only place in the scriptures where even limited authority is granted to the civil government to punish men for matters of faith and worship was under the Sinaitic Covenant. And that Covenant has passed away and has been replaced by the New Covenant. Under the New Covenant we firmly believe that God has ordained religious liberty and we are thankful for that mercy.
(Note: For further information on this position see Links: American Presbyterian Press, and look under Books for "Lord of the Conscience" a defense of religious liberty under the New Covenant, "The Hebrew Republic", an exposition of Biblical principles of government, and "The Divine Covenants", an exposition of the various divine covenants.)
The following links are to to books that expound on the subject of Biblical principles of civil government...
Vindiciae Contra Tyrannos (Vindication of Liberty Against Tyrants):
