That is really sad.
When the WT became a source of contention in my marriage, the thing that helped the most was to enhance and strengthen the other parts of the marriage and your lives in general.
It was very painful when my wife was baptized, but in the end I am grateful for the experience because it made me a better husband.
There is a time element here. It sounds like this is a relatively new development, and that this new change in status has not yet been processed and reached a steady state. It will take time to hash all this out. Especially with regards to the children.
In the mean time, provide as much stability in every other area of your marriage/life. Try to appreciate just how shocking and disconcerting all this is for here. She is likely questioning everything about you.
I know this is hard. But for better or worse, right? The hardest thing is to love when someone is unloveable, or who doesn't love you back, or rejects your love. But love isn't a feeling, it is a commitment, a promise. Make that a starting point, and I think you will have a good foundation for which to resolve the rest of the issues.
And who knows... when she sees that your leaving didn't change all the other things about you that she loves, maybe she will decide that leaving the org isn't the worst thing in the world.