Various Sues have received a blasphemy charge. It's been leveled at people who mangled various religious texts so badly that even the atheists cringed; or who created character replacements of deities (omnipotent deities cannot be out of character; they are immune) by turning the deity into a joke; or who displayed bigotry against various religions in various ways.
Religion is a difficult issue; and, in general, the PPC doesn't deal with it much because of how many different opinions people have and how you have to respect their viewpoints.
That said, though, we do deal with a lot of serious stuff that goes into fanfic; for example, agents have entered fics that contained homophobia, sexism, anti-disability prejudice, trivialization of rape, torture, and other forms of abuse and assault, and prejudice against races or cultures. Those things have been addressed with the same sort of high-quality writing I see when the issues are only grammar errors, anatomically impossible slash, or tru wuv with the resident cute guy.
Where would I draw the line? Well, there's a difference between an author writing from a viewpoint you don't agree with, and an author who's using that viewpoint to hurt others, or as a part of bad writing in general.
It's very much like the "your kink is not my kink" maxim for slash and erotica in general. Sure, you might get squicked by one act or another; but that's preference, and preference hasn't got anything to do with bad writing. On the other hand, if the author is doing a rape-equals-love story or turning a decent canon guy into a misogynist or just messing up the sex so badly that you're sure the act in question would be impossible even with three arms and two sets of reproductive organs... then that's spork-worthy.
Here's my suggestion for fics containing religion: If it's just an author with a viewpoint that you don't agree with, don't touch the fic. But if they are writing in a way that is obviously meant to be offensive, or shows obvious bigotry against a religious group, or makes so many mistakes that it's evident that they didn't do the research--then spork it, and show no mercy.
You know how people recommend that if you don't like slash, then you probably shouldn't be sporking it, because you have to know what good slash is to recognize bad slash? This is kind of like that, too. If there are religious issues in a fic, you should know about the religion in question; and, if you can find someone who holds that belief system, co-write with them or ask them to beta so you know you have your facts straight. While a comparative religions class can give you enough to recognize when a writer has neglected to do even basic research, all the little ins and outs and minority beliefs are generally only well-known within that religion.
I don't think we should stay away from religion just on principle, any more than we stay away from rape or child abuse or any other really heavy subject--but I do think it needs research and a good knowledge of what is bad writing or poor research, and what is merely a different belief system.