Medieval 1 had civil wars and although it wasnt perfect it had a great way of breaking a plan. I do hope no.2 has some form. I would guess that they cant do what they did in Barb invasion as you have to have extra faction slots to do it, unless they really will have 42 factions, with 21 being the normal ones and 21 being their counter rebel factions.
I really do hope there will be civil wars as evil men lay plans from within and seize power.