By siding with someone, you mean the disputes they bring up between each other?
Because I'll go ages without one of their arguments, and I'll be killing Sea Raiders and doing quests, and suddenly a companion with high morale will just blurt out that he's sick of things and wants to leave. I actually haven't been doing anything that I could imagine them being negative about. Haven't been at war or raiding anybody or anything.
So far I lost Alayen, Ferentis, Matheld, Artimenner, and Nizar.
I actually just realized that maybe I'm starting to have companion issues again because I'm playing the "More Companions plus Diplomacy mod", and that has been a wreck with the standard companions (the wrong people feud with each other, giving the wrong speeches, and they will talk about incorrect cities when I approach one). So maybe that's the reason this is happening. Could just be a bug. The answers you gave are useful but I'm thinking now that it's probably the mod.