OK, This seems like a fascinating kettle of worms.
It would be wrong, of course, to assume all churches are equal in their treatment, or mistreatment of transfolk. I mean, they can't even all agree on the tennants of thier Christianity.
On one hand, I agree partly with luv2Bfem's point that churches ought to be free to make their own descisions re. how they relate to us. But I cannot help thinking that the various flavors of Christianity are bound by the one commandment Jesus said was above all others, viz; Love thy God/Goddess (in my case), with all your heart, mind, and soul, and love your neighbor as yourself.
Looking at that rule, I think a huge number of denominations fall flat on their moral putukkas when they choose to treat anyone as an outcast, as somehow unworthy of thier rites. There are churches who feel that Everyone is welcome at the table of the big G. Look for those affiliated with the Evergreen Association if you need one.
That said, the lovely concept of freedom of religion means I can shake my head in wonder at those who practise segregation/bigotry/prejudice; and walk down the street to the nearest decent congregation, or buddhist temple or whatever floats my boat. And I like that.
As for me personally, since I went fulltime, I've found only acceptance in my community. Once I explained why my ID and me didn't look the same, my bank tellers have been really kind, my grocers are friendly, and my church - Palmer Church of the Covenant (the famous Howard Bess' Church) has been so accepting that I'm on the deacon board, and I preach about once every 6 weeks. Heck, some of my Church family showed up to my court hearing about my name change to "offer a friendly smile in an unfriendly place". Which is more than I can say about my blood family.
-Bri