It is not just religion. It is still a pretty homophobic society overall, EVEN with all the recent progress. It is still difficult to embrace a minority identity. It is in general difficult to be a member of a marginalized minority, whatever the group identification is - not necessarily sexual orientation. Some people find it more difficult than others.

My purely atheist grandmother considered homosexuality a disease. Thought that Tchaikovsky, probably one of the most famous gays of all times, was ill. So if your friend/passion grew up in that kind of household, completely free of religion but biased and prejudiced and uninformed still, she may have issues with her identity.

From the description you have provided, it can be both. I think. Not enough information to draw a definitive conclusion. I hope the situation improves for you and she becomes positively inclined. She might very well be conflicted and need time to come to terms with her attractions, and find some peace. There is nothing you can do to speed up this process.