It kinda depends on why you are going to a church. If it's just a social occasion, then it probably doesn't matter what you wear. Of course, some churches will be less tolerant than others for various reasons, but the point remains that if you are dressing for your own purposes then the churches purposes be damned. However, if you are attending church as a devout believer, then it is a worthwhile endeavor to seek out your own faith's stances on these things and try to be respectful of them. Cross-dressing is a deeply personal matter as is faith and we all need to find our comfort level individually. For some cross-dressing matters more than the restrictions of faith; for others faith matters more than personal satisfaction - either way, it is a personal matter and one that deserves personal contemplation.
To play along with everyone else, I am a devout person of faith and I wear women's clothes all the time - outwardly and under - though I have never cross-dressed and presented as female at church. I don't have an issue with cross-dressing at church, but I feel it's best to not cause problems. Maybe some think that that makes me a coward, but I have learned that not caring what people think about me is not the same as just not giving a damn about other people's feelings at all.