Full disclosure, I'm not a person of faith but I was raised in a very devout family.
The Bible never addresses the matter, and where it gets close, you have to do some pretty creative linguistic gymnastics to apply it. The closest it gets for trans women is eunuchs, but there is no concept of treating them as women so it's tough to see how one would interpret it, and which also means it is 100% silent on the topic of trans men because women were either virgins, wives, or whores, and any other qualities (like particularly masculine inclinations) were too trivial to mention.
Rather than spend any time pointing out the inconsistencies in the morality of the Bible to an unreceptive audience, I'll at least point out that there is one leader of a congregation who makes a case for being supportive:
http://www.huffingtonpost.com/rev-rich-rose/transgendered-sister-christ_b_934102.htmlAlso, as an ex-Catholic, I know that the position of the church (that they really don't mention unless they absolutely have to) is that if you have a moral conviction that the chuch got something wrong, you should not follow the church doctrine because it was made by man (and thus by their reasoning it very well could be wrong). So if you're "right with God" on being trans, it doesn't matter if the church says it's wrong. It may cause issues with the local bishop, which is just annoying as hell(as anyone who has tangled with a bishop knows), but it shouldn't cause a crisis of faith.
