This just happened to me too. Queen Procipinee of Pariden just hangs around after she burned her last city to the ground.
I don't think you should control a sovereign after you defeat them. You should just have that satisfaction that you finally managed to kill the bastard. It's ok if you can control them if they capitulate. But they should definitely disappear of they resign.
EDIT: I killed Queen Procipinee again after she was left standing there and now she's gone for good.