How old is she? It sounds like she will be 18 soon.
Be a friend and listen to her.Let her know that you are there for her and when she is of age - she is free to stay with you.
I am not sure what Christian school she is going to- but we are sending my daughter to one - not for this reason but because my daughter wanted to leave public school due to bullying and other social issues. It kind of depends of the Christian school but some although not necessarily supportive of this lifestyle are not judgmental. I hope this is the case for her so it will make it easier for her. Many teach to be kind and loving to each other.
In any case - you being a friend and offering a place when she is of age should help greatly.
As others say - it cannot hurt to tell your parents - they may not be able to directly do anything at this point - but knowing there are friends including adults there helping emotionally should go a long way. And for her to know that your parents would be open to her staying with them when she is 18 could go a long way.
I am sorry about this and wish there are more open Christian schools out there.