My fiance is Transgendered. We started out as best friends, transitioned into "Lesbians", and after his surgery and the hormones we're now both considered "Straight". At least to people who don't know us anyways. I think our families think we're nuts! Haha.
Anyways, in actuality I am a bisexual female and my fiance is a straight male. We met in high school and became very close over the course of those years. I fell in love with him because of his personality, his sense of humor, his loyalty and intelligence and so many other things. It didn't matter that he was a girl at the time. It didn't matter when he confessed that he loved me, but he wasn't comfortable being a girl. It wasn't my choice to make, and he made it pretty clear that he didn't want to lose me, but if I couldn't understand I was free to leave. It was something he had to do, and I respected him all the more for being so honest and brave and putting it out there. I have the utmost respect for anyone who makes that difficult decision and does what's best for their quality of life, instead of just living to everyone else's standards or expectations.
As for your friend, I will say that his dislike of Christianity may be due to a phobia of the hatred and nonacceptance that Christianity typically breeds. My guy is immensely uncomfortable with anything related to Christianity; we may not even be getting married in a church. It doesn't help that his mother is very religious either, but I believe many people of the LGBTQ persuasion are commonly uncomfortable with Christianity. Or at least uncomfortable with those who would persecute them or could harbor such hate for them because of who they are or who they love. It can be scary, being on that side of things, and knowing that there are people out there who could so easily hate you or even harm you without knowing a dang thing about you except for who you're with.
That said, each individual is just that: individual. Only your friend can know what he's going through, and it's his decision if he wants to share something so incredibly personal as that. He might feel scared, or like people are attacking or interrogating him and demanding that he explain his motives for being who he is. That's the only insight I can offer.
I sincerely hope you two will rekindle your friendship though, and that what happens in his personal life can stay personal and not interfere with what could otherwise perhaps be a rewarding mutual relationship. Unless of course he's really just a dick... in which case, do what's best for YOU, and try not to think about him and his issues, whatever those may be.
Life is too short to think about every person who has entered and then left your life. If there isn't room for him in yours, then stop making room by worrying or letting him occupy your thoughts. Move on, completely and fully. That's the best advice I can give you.