I'm not sure why Royals are such a massive pain in BM. They weren't that troublesome in the middle-ages, they could always be dethroned, exiles, or if need be assassinated. ;-) An uncooperative Duke, unless he's wielding military might to sustain his position, would most definitely be removed from his seat of power.
Y'all should read the wondrous A Distant Mirror. Man, the political intrigue, backstabbings and assassinations/murders in the 15th century were ridiculously entertaining ;-)