Being a Christian, having a Christian family and girlfriend, I can see how she could initially feel that way to begin with (and before people go off on an anti religious tangent..) Id like to say that these feelings dont have to be any reason for people not to accept transitioning in peoples lives. If you are true to yourself, and you both love eachother, there is nothing wrong there. You are not going out into the world and trying to do wrong.
I almost saw things for me as a test of my strength. Not that that was the reason I had to transition, but it was something I could get out of it. Only God is judge, noone on Earth is, so we shouldnt let a worry like this stop us from lovign someone, as she will be able to tell if it is right with God for her. And as you describe, things have been right up untill now. She may just need abit of time to accept and adjust (although, like Caseyyy said, if you two have been together 2 years, didnt she love you when you had a female body anyway...?)
My girlfriend questioned things at first, (because initially she didnt know about my past) but quickly came to realize I am just a normal person, what I have gone through isnt wrong, it was necessary and I still have a relationship with God as before.
I hope things go well for you with your girlfriend. Try to talk to her and get to see her worries so that you can try to guide her in the right understanding.