My husband was in a similar position. The only people there just for him were his parents. To avoid drama at the wedding we made a list of who he wanted most at the wedding. That was his parents. To accomodate them we ended up having to not invite a lot of the rest of the family. My best advice... DON'T DO SIDES. We had around 80 some people at our wedding and a lot of my family came. We set it up so parents were in the front row and then we talked to my family and had them arrange themselves to fit the rows directly behind both sets of parents, and then had everyone else fill in wherever (make sure there's few enough seats so they have no choice but to fill in both sides). Ultimately it is up to you, of course. There is always the chance of some drama.

PS. I just wanted to add that I am very proud of you for how you are dealing with your family situation. My husband won't go to therapy and is still in a lot of denial, I think, about how much their choices hurt him.