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The Founders believed that just law had two sources: divine revelation and human experience. In this regard, they were in line with political theory dating back to the Middle Ages and the Reformation era. You can find similar observations made by Thomas Aquinas. While Franklin and Jefferson were not orthodox Christians, the majority of the Founders were, with many in that group being Calvinists, notably John Witherspoon, Samuel Adams, and Patrick Henry. As such, their foundational principles were similar to modern evangelicals, especially Calvinists like D. James Kennedy, Chuck Colson, and Francis Schaffer.

Looking at the society in which the Founders and their immediate descendants lived, it was far more formally Christian than is contemporary America. Churches were the primary educators of the young, with virtually all colleges having religious origins. Many states had test oaths for public office that forbade atheists, and in some cases non-Christians, from holding public office. Until the early 20th Century, blasphemy was a crime, divorce was only granted in cases of adultery or desertion, and sexual relations outside of marriage were prohibited, as were abortion, birth control, and pornography. Such prohibitions were established in English common law and remained in force until the last century.

It is worthy to note that none of the Founders, even heterodox ones like Franklin and Jefferson, never lobbied to overturn these laws, for even if they may have rejected the miracles in the Bible, they accepted at least the utility of the moral code therein. For example, Jefferson authored a bill that would have made castration the punishment for sodomy. Virginia's punishment, though harsh, was less than the death penalty imposed by Connecticut, South Carolina, Vermont, and New York for the same crime.

The secularization of American society and the cordon sanitaire between government and Biblical principles that currently exists are ahistorical and have no roots in the writings of the Founders, irrespective of their personal religious beliefs. Rather, it has its roots from several sources, such as the legal positivism derived from philosophers such as William James, the Social Gospel movement in liberal Protestantism and its corollary in liberal Catholic social thought, the cultural Marxism deriving from the Frankfurt School in which the New Left is rooted, and deconstructionism common to postmodernism.

If you wonder how this nation has gotten to the point where perverts are welcome to Easter egg hunts, do not look to Jefferson, Madison, Hamilton, etc., and their philosophical forbears like Locke, Blackstone, and Montesquieu. Look rather to John Dewey, William James, Oliver Wendell Holmes, Earl Warren, Alfred Kinsey, Herbert Marcuse, and Jacques Derrida.

Of course the whole purpose of Thomas Jefferson's Bill for Proportioning Crimes and Punishments was to reduce the punishments for a number of capital crimes, but that's rarely acknowledged when brought up in this context. Moreover, it was actually a collaborative effort and not restricted to his own perspective (in other words, we can venture a highly plausible guess as to Jefferson's personal opinion, but cannot reliably infer that this proposed language reflected Jefferson's unique personal views).

The highly plausible guess we might venture as to Jefferson's own personal view is that which he stated three years later in his 1781 Notes on the State of Virginia, referring to sodomy, among other things: "The legitimate powers of government extend to such acts only as are injurious to others."

Moreover, it is worth noting that the 1778 attempt to standardize Virginia criminal law was rejected by the legislature. Instead, a 1792 statute maintained the British common law punishment of death, and then an 1800 revision knocked this down to 1-10 years in prison. Aside from that, let us also ignore, as is typical, that the official 1810 guideline to authorities seeking indictment for sodomy under the Virginia statute made clear that it was envisioned for and applied to instances of forcible assault, and that primarily with juvenile victims in mind.