Well, let's see. You have my total sympathy; I have been in a relationship like this before, and I've had a lot of counseling over the more harmful aspect of that relationship and its ending. I can't claim to say this is the right thing to do, but at least it's not the wrong thing to do.
It's absolutely her decision, and if you love her you need to come to terms with that. Let her know that she can choose who she wants in her life, and that you're okay with that. Sadly her family is NOT okay with who she chooses to have in her life, but since they believe their beliefs come from the Eternal Creator of the Universe it's unlikely that they'll ever accept you.
It really does come down to her decision: you, or them. But it's important to put the blame where it lies. The ones forcing this decision are not you, or her (she's happy with having both in her life) or even her family (since they're acting in accordance with their faith) but with their religion's policies. Again, since this is the literal Word of God there's no way to challenge it without making things worse.
Therefore, whatever choice she makes, she will be miserable because she will have to give up a significant part of her life. She will also likely channel that, consciously or unconsciously, into resentment and bitterness towards the ones she chose to stay with.
Your friend already has a strained relationship with her family. If, at this point, she is not yet fed up enough with them or devoted enough to you to have made the decision to stay with you already, I think your best option would be to let her go. If she makes the choice to stay with you now, then it will somehow be your fault that her relationship with her family was ruined; even if she doesn't believe so, her family will. It might be that this could be the last straw as far as her and her family is concerned, but if she knows that you will support her decision no matter what it is, the eventual result will be easier to cope with.
Set her free, and stay in touch. In time she will make the decision on her own terms, and it will be her decision with nobody else to make it for her. If she decides she's had enough then she can associate with as many gentiles as she likes, and maybe things will pick up between you again. If she decides to stay, then that is her decision for how she wants to live her life and there's nothing you could have done to change that.
I wish you peace and tranquility, and I think there's going to be a lot of tears in the next few weeks. I'm sorry you have to go through it but in the end, this is not something you have any control over. Give your love and support her in whatever she chooses to do, although it may break your heart.