CP,
Just to add a few words to the encouragement Grunt gave you, I was one of those who was inactive for quite some time but striving to get back in.
It seems that once the doubts and questions enter your mind, they never leave. You can try to suppress them, but they are there. Your wife has been in that "thinking" stage while she was inactive. Right now she's trying to be the perfect Witness once again, but I'd be willing to bet that her doubts are there, just below the surface, which is why she resists your efforts to such a degree.
I'm sure that she's thinking that if she could just get the proper counsel from the elders as to how to handle her "situation", all the doubts would go away. They won't.
Hopefully, she won't make any rash decisions. Just be patient and loving. Be the opposite of what she expects from an unbelieving partner...it may get her to start thinking again.