Crawford Gribben explains why:
This reading of Rutherford’s Free Disputation, set in the context of its times, challenges any idea that the modern, politically passive Presbyterian main- stream can be identified either with the theology of the Westminster Confession or that of its most influential divines.'”s Rutherford’s commitment to shaping an entirely Presbyterian world, where public deviations from orthodox faith or practice should be met with the most severe of legal consequences, is a world away from the political complacency of modern evangelicalism and the self- justifying myth it sponsors of the pluralistic benevolence of the Scottish Cove- nanting movement. Rutherford did believe in “liberty of conscience,” but, as the Confession argued, this was a liberty that provided no license to sin (WCF 20.3-4).
It is certainly true that we cannot simply read the Confession as a summary statement retaining the unqualified approval of all those who participated in its negotiation. The final text of the Confession was “a consensus statement, broad enough to be agreed with by Divines who held somewhat different views of the contemporary applications of the Mosaic judicial laws.” Rutherford seems to stand at one extreme of the Assembly’s range of opinions, arguing, with the apparent approval of the Commission of the Kirk’s General Assembly, that the OT judicial laws ought indeed to be the basis of the Presbyterian state for which they were working. Nevertheless, it is important to realize that Rutherford’s theonomic opinions were shared by many puritans who could not have endorsed his narrow ecclesiastical ambitions. Even those who favored a broader toleration of those orthodox Calvinists outside the Presbyterian system looked to the OT judicial laws as their program of action. Cromwell’s Rump Parliament established the death penalty for incest, adultery, and blasphemy.'” John Owen was prepared to argue that some of the judicial laws were “everlastingly binding.” The Fifth Monarchist radicals were famous exponents of a Hebraic legal renaissance.
However we understand the text and context of the Westminster Confession, therefore, we must recognize that the Confession is not committed to the separation of church and state in any modern understanding of that idea. The doctrine of the “two kingdoms,” where church and state operated independently but with mutual reliance on the law of God, did not at all favor a religiously neutral state. Thus the Confession charged the state with the highest of responsibilities: “The Civil Magistrate. . . 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 intire; 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, administered, and observed” (WCF 23.3). (Crawford Gribben, “Samuel Rutherford and Freedom of Conscience,” Westminster Theological Journal, 2009, 372-73)
All that pining for Constantine or Christendom that you hear from Peter Leithart or Doug Wilson should always evaporate after a weekend with Rutherford or the Stuart monarchs.