Forgive me if it has already been mentioned but I have not yet read all of the threads and posts here ...

If it is possible, I think it would be a good idea to not allow the recruitment of troops from the other faction when you have captured one of their castles.
If the Empire captures a Chaos-Stronghold it should not be able to recruit Marauders etc ...

Maybe in certain cases the only option you get after conquering a city/castle should be "Kill all the inhabitants" or "Enslave population" ...

I can see the Empire taking over an Elven city (maybe), but I don't think Orcs would simply occupy a Dwarven stronghold and don't do anything to the population ...