GTTM,
I feel your pain, and I'm sorry the WT cult appears to be destroying yet another family. I may not be the best person to give relationship advice; some would say that asking me for marriage/relationship advice is like asking Dr. Kervorkian for health tips.
In the past 20 plus years I have had several relationships. All of them were functional at many levels. However, I noticed issues of concern very early on in all of them - issues that if not addressed would have eventually ended the relationship. In each instance I discussed these issues with the girls. None of them improved. Oh, some did for a while, but eventually people are who they are. People don't change.
What I'm getting at is that I ended 4 relationships that were '90%' 'good' and functional because of what were relationship ending behaviors - to me - exhibited by these women. I would have rather ended them early than for them to degrade into the war of the roses. Still, ending a relationship with someone you care deeply for and that most of the relationship is good, takes an emotional toll. It takes an ever larger emotional and financial toll the longer it drags on.
No one can determine for you what is the right course, as only you know whether the 90% will stay as it is or if it will consistently degrade until it is only 10% good. Or that it levels off at 70% or 50%. You are the only one who knows what you can accept and deal with for the long term. You need to make whatever decision based on your wife staying in the cult.
Me? I've got very little patience for being with someone or some situation that is causing me pain. I would rather be by myself; but that is me.
Good luck
DJS (aka Dr. Kervorkian Relationship Guru)