Apparently Kevin Smith made this comment that Jay was bisexual so that there was more room for joking around (apparently in other movies, Jay did show signs of being gay).
Anyway, I think that the point was that the movie touched on some of the big issues with the church in some form or another: Abortion (Bethany's job), euthanasia (God stuck on life support), homosexuality (the varios things mentioned in this thread), racism (Rufus and his problems), and gender inequality (Serendipity and her problems) just to name a few.
The fact that there are such things going on with the main characters, who are all chosen by God, kind of seems to say "things aren't quite a ridged as you seem to think!" Rufus, Serendipity, and the Voice of God were all shown to swear, drink, loose their tempers, and make mistakes. Heck, Jay and Silent Bob were chosen as the prophets and the Voice of God pretty much seems to dislike them.
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