Personally, I don't think your friends were being very good friends to you. People don't have to be exactly the same to be friends, but they do need to respect each other. It sounds like she wasn't respecting you at all. I don't think you need to feel guilty over standing up for yourself.

Does your college have a Christian students group you can join?

Have you talked to the other friend, the one that hasn't been sending your cruel notes?

I promise there are people out there that have different beliefs from you but still respect you.