I think the thing there is, wierd, that there's a disconnect, at least in my mind and definitely in the mind of others, as far as I know, as to whether what the Spirit desires actually matches matches up to what makes people happy. If you're just saying that people are happy when God is with them or whatever, regardless, and as a result they won't want anything else...well, that sounds disturbingly similar to either wireheading or mind control via emotions. Which are both, at least in my values system, undesirable. The second is creepy, the first meaningless.
Basically, I have fundamental disagreements as to whether the principles given by God are in fact the necessary principles for a society of immortals to live harmoniously for eternity. I could talk about how conflict is inherent in human nature but that's easily dismissed as just being sin (I
like debate and conflict of the mind, be it in games or speech; I know some people hate losing, but I just enjoy the process). Going against this, then means that I consider my views more correct than that of others, a fact true of literally everyone because otherwise they wouldn't hold those views in the face of anyone having a different one. You could say it means I hold myself above God, and I would disagree; I just hold an all-perfect being to a
very rigorous standard, and will be gravely disappointed if he does not meet that standard. I have no frame of reference besides my own to base this standard off, so by definition I cannot hold God to His Own standards. That would defeat the point, anyway.
Christianity ends up looking self-referential if you try to base it on it's own assumptions, able to dismiss arguments in much the same way conspiracy theories do. Any evil humans do is evidence we have a sinful nature; when people who proclaim themselves to be true Christians do so, they were just liars or not very good Christians(I agree with that, by the way, since I still think Jesus was overall a pretty cool dude whether or not he was a lich); Christians who do good are evidence that God's work is at hand; Non-Christians who do good are evidence that He has left his mark on us, and that we are redeemable. Any time my beliefs of what is good differ from the Bible's, that proves that I am wrong, because God is perfect, and He knows best, because He said so. And since He is perfect and good, He would never lie, nor would He be mistaken.
That said, I grew up in a house relatively hostile to Christianity, where I am less liberal than my parents despite my goal in life being literally to achieve immortality, via nanobots. I may accidentally become the Anti-Christ if their hosts reject them leaving strangely spiral or six-shaped marks. *shrug*
Also, two things to note: 1, Religion has been shown to improve the psychoemotional health of people who have such beliefs. I'm guessing because knowing your purpose in life/the meaning in life/not worrying a shitton about death and nothingness like I might sometimes when I'm not distracting myself is more healthy than the alternative.
2, Mother Theresa may have been having an ongoing crisis of faith for the last fifty years of her life, based on her journals and the like.
As for people made uncomfortable by the less hospitable branches of the Christian faith; people are assholes. People will always be assholes. They will always find an outlet to be assholes. I find the sort of atheism that claims all religions are horrible and bad and you should feel bad for being religious and you effectively contributed to genocide and warmongering during the crusades and promote hate and intolerance by your implicit support for all the other branches of your religion including the bad ones, to be horribly dishonest, disrespectful, contemptuous towards people's beliefs and by extension (quite explicit extension, much of the time), the people who hold them, and generally also assholish. Christianity just has a persecution complex that tells them they're good people for being attacked in that way, so they don't get hurt emotionally as much. Key words being as much.
Religion causes wars and fosters hatred, and it creates community, encourages charity, and proposes answers to questions we cannot answer. Some of these can't be answer for the same reason I can't truly be certain a perfectly agile pink unicorn ghost is behind me, but they usually have somewhat more relevance to the human psyche.
Oh yeah, and for homosexuality: I'm pretty sure (I haven't actually read articles on it, but I get the general impression from adjacent studies) that while genetics plays a part in how susceptible you are to 'catching teh gay', it also has to do with environment. And simple errors in the code; I'm fairly sure being transgendered is basically a genetic defect that causes your mind's perception of gender and your physical gender to end up being desynchronized. Doesn't mean they're bad people, and it doesn't necessarily mean the fix is messing with their heads, but still. Environment plays a pretty big part. How I have no idea.
Bah this keeps getting longer: Animals do that too, Icefire!
It's just that they disagree as to who is the leader of the pack, and
then kill. Or whether you're allowed to look at it funny, like hippos do. Plenty of birds steal things because they're pretty (and you never asked the baker, so he's not exactly greedy :p). And plenty of animals deceive, whether in mating calls or just plain sneaking.