The issues are much deeper than the religion. I would venture a guess that most people in this organization have no real concept of what they truly believe or what they are teaching. Your wife is caught up in the package. That's right, the package. To be a witness is to subscribe to all the requirements along with all the benefits. And, contrary to what most would post on this board, there are many benefits, particularly social. So, when you decided to walk away from the ORG, you were essentially cutting away the social aspects of your family. Now, for me, I don't really care about the social things. I am busy at work, have a good close knit circle of "buddies" that I can go eat lunch with or shoot the breeze with, so if people in the hall think I'm "bad association" (although I am still as virtuous and moral as I have ever been...cause I choose to be) than fine. But, for a wife, to not be part of the gatherings, and hosting the CO or the speaker after the meeting, or hang out after the asembly, is REALLY bad.
So, suggestions....reach out the her family. Particularly those members who are not witnesses or are boaderline. Get on Ancestry and look up family members she's not aware of and reach out. Find out what interests she has (if any) other than the ORG. Get your kids involved in music or something else that will require your attention, especially evening hour attention. This will gradually fill the void of the ORG social world that she has become accustomed to.
Additionally, don't take it personally, as hard as that may be. If she loves you, than she loves you. People are typically creatures of habit, you are challenging what she has become accustomed to and that is hard. The ORG has demonized dissenters. Reach out to her on a personal level. Get her flowers, plan a long weekend. Be the integral part of her social world.....just some thoughts.