Really stupid question, but does your sm_factions still have the shadowed_by, shadowing bit in for the e_e_rebels?

I've had problems in game before playing e_w and e_e when I destroyed buildings and garrison in besieged settlements I knew I was going to lose. Had assumed it was to do with game then trying to revolt to e_w/e_e rebels
but clashing with take over by besieging army - but from your description CTD could be explained by this bug.