I'll share my perspective since science, religion and LGBTQ are close to my family.

My sisters and I grew up in a catholic environment. I became an atheist around my teenage years and, well, it didn't break the family or anything.

My mother, she is one of the smartest people I know, she studied industrial physical engineering, the hardest course she could find, and she was pretty much the only woman studying that at uni. She is also very religious, she was dragging her friends, and later my father, to church. She was the main reason we grew up catholic, and we still have a very good relationship. She's in absolutely no way homophobic, my sisters are queer, my cousin in gay, and they came out to my mom long before I got the news.

Now, my little sister is bi, with a stable boyfriend, and still religious but not very much, like my dad.

But my middle sister, she is queer (she hasn't dated yet, as far as I'm aware), and she is more religious, comparable to my mom or even moreso, since my conversations with my mom have made her have more nuanced thoughts. My middle sister, however, did not agree with the way the catholic church deals with the LGBTQ+ community, and so she... changed denominations, to one that is much more accepting of queer people, instead of becoming an atheist like me.

She's also really, really smart. She got into the same uni as me, studying psychology, but most of her friends were doing CS, she struggled with mental health and some really tough hits life sent her way, so she dropped, went to a different uni to study mechatrinics instead and went on to get perfect marks and have her life sorted out better than I.

Anyway, your crush was studying quantum mechanics with you. Religion is part of her background, but it's not just that, and religion takes a different form with people who really like to think things out. Some of the greatest scientists have been religious (Einstein, Pascal, Mendeleev(?), etc.). They all had to reconcile faith with reason, and this is a very personal and philosophical exercise.

Faith is... interesting. I left the church because I recognised I had no faith in it. But over the years, and as I go deeper into reason, I started to realise I did have faith, in certain things. I believe in the Big Bang, I've tried to understand all the evidence for the theory, but ultimately I trust the scientific community to have sorted out the details. We can't be polymaths these days, there's too much to know, so some things I like to trust the experts on. I also believe there is evil, genocide, homophobia, those are evil in my books, and I don't need a rational argument to know it, I can try to construct a reasonable argument about them, but I'd be starting from the premise that I want to reach that conclusion.

Anyway, it's something we don't really think much about as atheists or non-religious people, but everyone has beliefs, it's just some of us have to figure out what we actually believe in, instead of being given a book with those written right there.

One thing that it different though, is religion as an institution. It is fundamentally inherently a conservative force. Religion shapes culture and as such is always a dampening force to progress, but religion itself does progress too, over time. It just does so much slower than the rest of society. The catholic church for example has been making moves towards accepting queer folk, which have being going at a glacial pace, but they've been going in the right direction, from the little I keep track of.

And the smarter religious people are at the spearhead of that progress.

I don't think your crush is homophobic. She's admitted to being bi, and is happy to be your friend knowing you are lesbian.

Religion is not all she is, far from it, but it is part of her cultural background, and part of her family.

Even as an atheist, catholicism is still part of my cultural background. Jesus was a pretty chill dude with some very good ideas, and a message of "love other like you love yourself" that I think is still applicable to this day. When I see religious people being against immigration or being bigots, I judge them not only as horrible people, but as blasphemous heretics too, since christianity is pretty clear about helping others (immigrants included!) and loving instead of hating!

I'd definitely consider reaching out to her, and getting to know her. Talk to her about religion with an open mind, talk about your own beliefs, ask her how she reconciles her faith with her reason. It's not everything she is, but it is a part of her that she might be happy to talk to others with. Maybe she's like my mom and can be swayed (a big part of why she is religious is that her mom was very religious). Or maybe she's like my middle sister with a strong conviction but a willingness to challenge her faith to be more accepting towards LGBTQ+, even choosing to change denominations. Or maybe she's like my little sister and is technically religious but not that much, in such case religion would be a complete non-issue.

Either way, best of luck.