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.
OTOH, none of the states enforced church attendance, all permitted the free exercise of religion, and most (Massachusetts and Connecticut excepted) disestablished the churches that were tax supported while they were under the British Crown. Even the last two states ended the establishment of the Congregational Church by 1835. Despite the disestablishment of the church and freedom of religion, the philosophical underpinnings of American law and the political order drew from Christian sources.
The abolition of the laws prohibiting sexual activities outside of marriage occurred gradually, mostly in the early and mid-20th Century, as legal positivism gradually replaced the Biblical roots of common law and the relatively new field of psychology perceived sexuality in terms of behavior or pathology rather than sin. Additionally, the effects of popular mass market entertainment and a reaction to the excessive prudishness of the Victorian era set the climate for a shift of popular opinion away from traditional sexual mores toward permissiveness.
Neither evangelical Christians nor other adherents of traditional, Biblically based morality that are out of sync with the beliefs of the Founding Fathers and the laws and customs of this nation in its first 150 years of existence. Rather, it is the secularists and libertines, including those who pose as conservatives on Free Republic and elsewhere, who are the opponents of the political and moral philosophy on which America was founded.