If she is determined to stay in, than I would say make a clean break as quickly as possible. If you have hopes of staying together, I would sit her down and make one final attempt to get her to listen to reason, explain what you've learned in as calm and loving a way as possible, then let her make up her mind. In my opinion, a happy marriage between a half-hearted witness and an unbeliever may be possible, but a happy marriage between a zealot and an unbeliever probably isn't.
My wife and I were together for two years after I let her know I didn't believe this was the truth, and those two years were agony. My regret is that I didn't leave immediately when I realized that having a happy relationship had become impossible. Don't go through with years of unhappiness (on both sides), just for it to end in bitterness anyway years down the road. You have a lot of life left ahead of you. Don't waste any of it.