When a region is blasted to hell, the #1 priority you need to work on is loyalty. (Control is only important to keep it from revolting immediately. Setting militia can at least delay a revolt by a turn as the peasants lynch them.) While you have courtiers and diplomats working on loyalty, it's a good idea to have 2-3 units doing constant normal police work. (More if it's a high-poulation region.)
Once loyalty is above 25%, you're pretty much safe holding courts. At that point, hold just courts until loyalty is ~40-60%, then start doing merciful courts to raise morale until it's about where loyalty is (continuing the constant police work to keep control up, and if that's not enough, then alternate in a few harsh court sessions). From there, just keep working on the region—unless someone decides to hang rebels and crash morale or something equally stupid, once you're above 30-40% loyalty and morale, you're usually in the clear.
