The following is a quotation from Sam Waldron (in his Exposition of the 1689), who includes a quotation from John Murray:
A serious objection to the separation of church and state is that civil authority must rule according to the Word of God. If it is so to rule, how can it permit religious freedom? For instance, the Second Commandment forbids idolatry. Is it not, then, the duty of the civil authority also to forbid idolatry?
Here a crucial distinction must be enunciated. It is certainly true that civil authority is subject to the Word of God, but this does not mean that it is the duty of the civil authority to enforce every part of God’s Word with its own authority. Several illustrations will make this clear.
Ephesians 6:4 asserts, “And fathers, do not provoke your children to anger, but bring them up in the discipline and instruction of the Lord.” The civil magistrate ought not to take it upon himself to bring up children. Not because the Word is not his authority, but because he is not a father. The exhortations to pastors in 1 Peter 5:2 are not to be implemented by the civil magistrate for the same reason. A civil magistrate is not a pastor.
John Murray well says,
“Since the civil magistrate is invested with this authority by God and is obligated by divine ordinance to discharge these functions, he is responsible to God, the one living and true God who alone has ordained him. The magistrate is, therefore, under obligation to discharge the office devolving upon him in accordance with the revealed will of God. The Bible is the supreme and infallible revelation of God’s will and it is, therefore, the supreme and infallible rule in all departments of life. The civil magistrate is under obligation to recognize it as the infallible rule for the exercise of civil magistracy.
It must be recognized, however, that it is only within his own restricted sphere of authority that the civil magistrate, in his capacity as civil magistrate, is to apply the revelation of God’s will as provided in Scripture. It is only to the extent to which the revelation of Scripture bears upon the functions discharged by the state and upon the performance of the office of the civil magistrate, that he, in the discharge of these functions, is bound to fulfill the demands of Scripture. If the civil magistrate should attempt, in his capacity as magistrate, to carry into effect the demands of Scripture which bear upon him in other capacities, or the demands of Scripture upon other institutions, he would be immediately guilty of violating his prerogatives and of contravening the requirements of Scripture.
The sphere of the church is distinct from that of the civil magistrate. . . . The church is not subordinate to the state, nor is the state subordinate to the church. They are both subordinate to God and to Christ in his mediatorial dominion as head over all things to his body the church. Both church and state are under obligation to recognize this subordination and corresponding co-ordination of their respective spheres of operation in the divine institution. Each must maintain and assert its autonomy in reference to the other and preserve its freedom from intrusion on the part of the other.”
Why is the civil magistrate not to enforce the first table of the law [the first half of the Ten Commandments]? Because he is somehow not subject to the Word of God? No! Because it is not his job!
…Besides what has already been said, three comments are appropriate. Firstly, some limitation of the term ‘evil’ must be assumed in Roma 13:3-4 since the civil ruler is obviously not to punish private evil or evil of the heart. Secondly, interestingly enough, when Paul goes on to speak of the law in Romans 13, he speaks only of the ‘second table’ of the law. Thirdly, the historical context of Romans 13 makes incredible the idea that civil rulers are to punish religious evil. Paul is not speaking ideally in Romans 13, but of the actual conduct of the Roman government as it ruled in his life. Without doubt, the Roman emperors were not a cause of fear for religious evil behavior (Rom 13:1, 3-4).