It really depends, I think, on if she truly believes in it or if she is going to leave it.
I am a non-believer (like you, of any religion) and I married a Witness. When we met, he was an active Witness -- but in our earliest conversations he told me he did not believe in it and was just going to appease his family. He stopped attending meetings after we started dating seriously. He did not stop going BECAUSE of me, nor did I ever ask him not to go - it was his decision, and I was just there for encouragement. He fortunately was never disfellowshipped, so he is now just inactive and can still have a relationship with his family.
Yet planning our wedding was the most stressful time of my life because of that religion. We were not allowed to have Witness family members in the wedding, and many Witnesses with whom my husband was close refused to come. It was hard -- but in the end, wholly worth it!
So I guess my advice is this: If she is willing to put YOU first, then I wouldn't just run. But the problem is, if she still actively believes, she will not put you first. You should also know (if you don't) that in many cases, if she marries you and stops attending, she could be disfellowshipped and would not be allowed any contact with her family. Now, she is a big girl, so she should know/understand that. But if that happens, people will blame YOU. She might later blame you, and you might feel guilt yourself -- not to mention all the Witnesses who will blame you and cast you as Satan. It is a hard position to be in.
I don't think there's a clear right-or-wrong choice. Running like hell would probably be in the easiest option, especially (I think) if she will not put you first. In a marriage, YOU have to be her priority (and she has to be yours), not that crack-head religion. If she won't do that, then don't marry her... because you will not be treated right. However, if she will put you first, if you two are truly in that life-long love that you just KNOW you cannot leave, and if you are willing to put up with A LOT OF CRAP - then it is certainly your decision, and perhaps love will conquer all.
I know it did for me.
Best of luck, and welcome to the board.