I exhort therefore that first of all, supplications, prayers, intercessions, and giving of thanks be made for all men: for kings, and for all that are in authority, that we may lead a quiet, and a peaceable life, in all godliness and honesty. (1 Tim. 2.1-2)
How is that we are to pray for our civil magistrates? That we may live a quiet and peaceable life? Yes, but "in all godliness and honesty." How did older Puritan and Reformed divines understand this guidance for how we are to pray? The Westminster Divines understood this verse to support the proposition inferred from the second petition of the Lord's Prayer -- "thy kingdom come" -- that the Lord teaches us to pray that "the church [may be] furnished with all gospel officers and ordinances [and...] countenanced and maintained by the civil magistrate" (Westminster Larger Catechism Q. 192). So far from this verse supporting the modern doctrine of "separation of church and state" (understood to imply that the state must be divorced from any support of piety), this verse in fact, according to the Reformed historically, teaches that our prayers ought to be that magistrates would promote piety towards the end that we might live piously, quietly and peaceably.
John Calvin writes on this passage:
That we may lead a peaceful and quiet life By exhibiting the advantage, he holds out an additional inducement, for he enumerates the fruits which are yielded to us by a well regulated government. The first is a peaceful life; for magistrates are armed with the sword, in order to keep us in peace. If they did not restrain the hardihood of wicked men, every place would be full of robberies and murders. The true way of maintaining peace, therefore, is, when every one obtains what is his own, and the violence of the more powerful is kept under restraint.
With all godliness and decency The second fruit is the preservation of godliness, that is, when magistrates give themselves to promote religion, to maintain the worship of God, and to take care that sacred ordinances be observed with due reverence. The third fruit is the care of public decency; for it is also the business of magistrates to prevent men from abandoning themselves to brutal filthiness or flagitious conduct, but, on the contrary, to promote decency and moderation. If these three things are taken away, what will be the condition of human life? If, therefore, we are at all moved by solicitude about the peace of society, or godliness, or decency, let us remember that we ought also to be solicitous about those through whose agency we obtain such distinguished benefits.
Hence we conclude, that fanatics, who wish to have magistrates taken away, are destitute of all humanity, and breathe nothing but cruel barbarism. How different is it to say, that we ought to pray for kings, in order that justice and decency may prevail, and to say, that not only the name of kingly power, but all government, is opposed to religion! We have the Spirit of God for the Author of the former sentiment, and therefore the latter must be from the Devil.
If any one ask, Ought we to pray for kings, from whom we obtain none of these advantages? I answer, the object of our prayer is, that, guided by the Spirit of God, they may begin to impart to us those benefits of which they formerly deprived us. It is our duty, therefore, not only to pray for those who are already worthy, but we must pray to God that he may make bad men good. We must always hold by this principle, that magistrates were appointed by God for the protection of religion, as well as of the peace and decency of society, in exactly the same manner that the earth is appointed to produce food. Accordingly, in like manner as, when we pray to God for our daily bread, we ask him to make the earth fertile by his blessing; so in those benefits of which we have already spoken, we ought to consider the ordinary means which he has appointed by his providence for bestowing them.
To this must be added, that, if we are deprived of those benefits the communication of which Paul assigns to magistrates, that is through our own fault. It is the wrath of God that renders magistrates useless to us, in the same manner that it renders the earth barren; and, therefore, we ought to pray for the removal of those chastisements which have been brought upon us by our sins.
On the other hand, princes, and all who hold the office of magistracy, are here reminded of their duty. It is not enough, if, by giving to every one what is due, they restrain all acts of violence, and maintain peace; but they must likewise endeavor to promote religion, and to regulate morals by wholesome discipline. The exhortation of David (Psalm 2:12) to “kiss the Son,” and the prophecy of Isaiah, that they shall be nursing — fathers of the Church, (Isaiah 49:23) are not without meaning; and, therefore, they have no right to flatter themselves, if they neglect to lend their assistance to maintain the worship of God.
Thomas Cobbett, The Civil Magistrate's Power, pp. 35-36, writes likewise:
...civil rulers by their office and place, now in the days of the New Testament, are to look to matters pertaining to godliness; whether doctrinal, or practical, so far as acted by the outward man, and appearing in outward view in their life or the like, as well as they are in the like way, to look to the matters of honesty. As he that is taught to pray that he may lead a quiet and peaceable life in all godliness, and honesty, prayeth that he may lead a life in all godliness and honesty (without which to pray for peace and quiet in any other life, or to pray to be let alone unmolested, in any ungodly or dishonest way of his life, even but to ask leave and liberty to sin). So he that prayeth to the Lord, for all that are in highest civil authority, as for kings or the like; for this end, that he may live in all godliness and honesty, quietly, and peaceably, he prayeth to God, to cause the persons in such civil authority, to further by their civil authority such an end, to which under God they are an external means, and surely then he prayeth, that persons in civil authority may in such sort attend and look to matters as well of piety, as of honesty, appearing in any acts or ways of their subjects' lives; as that their subjects may in such godly and honest acts and ways of their life and in no other enjoy peace and quiet.