I'd like to cut in to say that I really don't think this reads as that religious at all. Sure, some of the names are biblical and she prayed once, but I don't think that it makes the story that religious. If that's something you're going for, I'm all for it! I love religious themes so long as they aren't whacking me over the head. In fact, I think it would be interesting if you made religion more present in our girl's life and relate what it means to her and how it's helped her develop. I am religious, so obviously I'd want it to be a positive message, but if you're not religious, you could explore the positive aspects of it for a young girl and the negative aspects.
I think a bigger problem with the story is, as someone commented earlier, that almost all of the little snippets you shared are about her being worried about her body and being harrassed, but it almost feels as if the text is objectifying her rather than viewing her more compassionately. I think you only had to say one time that her body was more developed than the other girls and that some of the boys leer at her.
Another problem I had a bit with the text is that all the boys are little monsters. I don't think it's interesting to portray all of them that way. I know there was a boy who she had a crush on once who seemed sweet, but I think it'd be great to have a few boys in the school who are just neutral or kind toward her, too. Maybe make one share a pencil with her because she forgot to bring one. Maybe have another open a door for her when she's carrying books, etc, etc.