Homosexuality is as old as mankind, or even older. Religion is not.
The Founding Fathers, well-educated and well-travelled men, would have been very aware of homosexuality, but yet they make no mention of banning or outlawing it in the Constitution.
But the Constitution does say, "Congress shall make no law respecting an establishment of religion, or prohibiting the free exercise thereof;" thereby limiting the power of religion by 'making no law respecting establishment of it' (my paraphrase).
The point is that the Founding Fathers were so unconcerned with homosexuality that they didn't even mention it, but they were so worried about theocracy that they placed a caveat in the First Amendment.
I'd say that pretty well delineates where the Founding Fathers' concerns were.