They'll get plenty of protection in the dungeon after I crush their revolt and revoke their titles. Maybe even a stay in the oubliette if I'm lucky (that event doesn't fire enough as I'd like TBH).
While it is a sound strategy now and then to get rid of troublesome vassal, it is also quite destructive as a policy. Imprisoned character will like you less and thus you will get less tax and levy from him. It is fine if he is alone, but if you imprison them all - you are undermining your own power.