She seriously needs to find a different church!!! Yeah, I know, not bloody likely.
About 7 years ago, I started my struggle with my faith in God. I have since found what I will call my foundation and am re-building everything else from scratch. I grew up "Evangelical, born-again Christian" and for me about 99% of it is a lot of man made bull shit.
The pastor I had during my high school years played a significant part in me being able to finally see all the bs. One of his big pushes, was that he was just a man, giving his version of what he read and studied and he could be wrong. He encouraged us to study and look into on our own. After that, I never did put up with arogant, high and mighty preachers.
I no longer attend "church", but I do still have my faith. I no longer call my self a "Christian" because I don't want to be associated with "religion" for so many reasons. My mother sees my (and my brother) as lost souls because we don't subscribe to ALL of her beliefs... so be it.
I have been to "Christian" counceling and have gotten very different advice and had different experiences than what you faced. However, what you faced is not all that uncommon in some of the more militant churches, which even before my "crisis in faith" I stayed well away from.
My advice is for you to interview a few Christian marriage/family councelors, that are not in anyway affiliated with your wife's church. If you find one that doesn't creep you out or piss you off, try going to that one with your wife - knowing people like your wife, the title of "Christian" holds more weight and she won't be as ready to dismiss what they have to say.
A couple verses that I have used, both for myself and to stop others (mainly my mother) in their tracks are Matthew 22:37-40 and Romans 14.