As much as I like plot twists, I really liked the Captain and I'm skeptical about his replacement.
He went out in blaze of glory. What more could a character ask for?
As for his replacement though, i share your skepticism. But it could be a good thing. If Beckett and Castle's romantic tension eases up a bit, or goes full blown romantic, due to the events of last season they will have to replace that with something. And Penny Johnson Jerald seems like a excellent choice to play a more adversarial captain. Someone who might not appreciate Castle's presence quite as much as the established characters have learned to.
The characters might have to end up fighting tooth and nail to keep Castle's consultant post intact.