That is the first I've heard of her being homophobic, so of course as you do in this day and age, I googled about that.

Found some 'interesting' stuff online, and one or two quotes that she made on the subject. They don't appear to be homophobic as such (as they don't seem to evidence a fear or dislike of homosexuals), but certainly show a great deal of insensitivity, stereotyping and and just plain ignorance / stupidity?
I'm not sure about her locking them into certain roles, when it comes to the dragonriders, it appears that yes she has locked different sexualities to different dragons, for one reason or another, but this doesn't seem to necessarily be reflected elsewhere, though I haven't read many of her other books outside of Pern to get a good impression of that.

Her comments certainly make me respect her less, but I still enjoy the books as they are, and think I will continue to enjoy them.

Regarding the religious aspect, I have to admit that is something I hadn't really noticed before. I don't personally see that as a big issue, of the books I have read in the fantasy / sci-fi world, many have a God, many have multiple Gods and some have no Gods, and outside of where the God/s play a part in the overall plot, I don't generally notice them a great deal, or their absence.