Oh Leah, this is a nasty experience, and one I can relate to. A male friend of mine became a father and told me not to come round because his mother-in-law was kind of "traditional." Quite a slap in the face.
Like you, I think I've had a wonderful transition. But I suspected that someone would ultimately do something like this to reject me, and yes, it did happen. It was just one person, on the periphery of my friendships, but it hurt for a couple of weeks at least.
Unlike you, I don't really care if people are uncomfortable - I think one is lowering one's value by expecting that people might or could be uncomfortable, and I would rather use the opportunity to gently confront people and educate them.
If this is one of your closest friends, it's a hard blow indeed. All I can suggest is that you meet him and explain how much it hurt. We trans folk do not need to avoid an appropriate type of confrontation with religious people - by avoiding them this just perpetuates an ignorance over the diversity and validity of all people.
As for the friend who did this to me, he was actually projecting his discomfort onto another family member and using that person as the excuse, and this may be the case with your friend too? This too is worth discussing with him.
Leah, while you might have to painfully prune a few people from your circle, try not to take is as a personal rejection. Your friend may not be strong enough to feel able to justify his choices of friends to his parents. Try a bit of dialogue knowing that you're stronger than he is.
Good luck girl!!
Julia
PS - my "ex"-friend called me after a couple of months, came round, apologised profusely for being a d**k (his words), and we're back on track.
