Vincent, I think you'll find that almost every church has lots of hypocrisy. But as the saying goes, there's always room for one more. The same is true for any other organization that seeks to promote virtue (say, the Sierra Club, to take an obvious example).
Anyway, I'm not sure exactly what your situation is, but the way I came out at church was to start by coming out to people I was pretty sure would be supportive and who were closer friends (actually, very close friends). I felt that they needed to know. They suggested some other people to speak to before I spoke with the rector, who gave me some insight into how the rector might react, and when I finally spoke to her, I made it clear that I needed to be able to come to church as a girl, because it was causing so much stress to come as a guy. Basically, I tried to make honesty my guide. I came out to people explaining that this was important to me, something that wouldn't change, a big part of my life, and something I felt was getting in the way of my relationship with them and the church, and asked for their help. It seemed to work well. This might be harder for you if you aren't that close to people there right now, but maybe you can do something similar.
I'm not sure if I totally agree with Kate's approach; I think it depends on your personality. What I worry about is that it isn't LGBT rights in the abstract that they ought to be worrying about, but the ability of their members to have life in abundance, regardless of any label someone might stick on them. I have seen some churches that are self-consciously "open and affirming" (i.e., towards LGBT folk) but make you feel like a token.
I guess what I'm saying overall is that it doesn't matter if they accepting of trans people, only that they are accepting of you.
