Live Your Own Life
As a Junior in college, you ought to be living your own life. That counts for who you date and "fall in love" with as well. If your girlfriend needs to keep you a secret, then she is either very religious (and is afraid of the sin) or she is very immature. Your letter suggests the latter.
You Can't Change Her
You cannot change her relationship with her father you can be supportive, you can be loving, you can continue to be a doormat but she has to face her father and her own choices herself.
Love Means Not Being Secretive
Until then, I would make it clear that the current situation is unacceptable. Why would you want to stay a secret if you "love" her?
I put love in quotes here and above because to really love is the most mature of feelings and commitments. If you two are in love, then keeping it from her parents is really impossible. I suggest that her "love" is a guilty pleasure at this point.
She needs to decide whether you are worth facing her big issues. That's her call.
I'd hit the road, pal. Find someone who knows how to really love and is grown up enough to face it.