Hang in there, man. As was said before - try to engage only with her natural personality, when the cult personality is controlling her, just shut down, or if she comes at you all of a sudden, you might be able to deflect by asking her what brings this up. It's so difficult not to just jump right in with all the proof that it's a cult when you're being challenged, but sometimes you have to make a strategic withdraw to win later. I'm the type that I like to debate and present a solid argument/proof of my point, but convincing the other person is secondary to beating them. It's really tough to switch gears to letting some bit of completely flawed reasoning go unchallenged in the interests of convincing someone over presenting a good argument.
Also, while it may be true, pushing the 'mind control' business might not be the most effective approach. No one under mind control actually believes they're being controlled or manipulated - that's why it works. So when you say that, you're directly and succinctly challenging the very reality in which she lives. This is like someone coming to you and asserting that your children are hallucinations and that you're schizophrenic - you'd probably not take it very well if they continued to press the issue.
When asked what your problem is with the cult, you might change to something like "my problem is that it seems to be the source of all the arguments that I have with the woman that I love." It's tough to hold back and remain calm, but one of you needs to and it's sure not going to be her.
I haven't dealt with anything on this level yet myself, but I'm sure it's coming. Thanks for sharing.
Oh, and heisenburg - maybe you should start another thread. It's rather insensitive to come in here and defend the cult that's trying to break up someone's marriage.
