Remember that part of the problem is that women in the Borg have no identity except that of their husband's. It will be hard to stop being an "elder's wife."
What Blondie said here is important to remember. I wen't through similar things with my ex. While, I'm not saying that we would have been able to overcome our issues anyway, I will say, that had I been more mindful of this, I could have had more peace. It bothered me tremendously that she just "wouldn't get it". So my advice is, expect that she won't "just get it". Give her time, (a lot of time, if your family is worth saving, and it sounds like it is). Help her build an identity outside of the organization, really, this will help make it easier. It's about both of you.
j