If I read the rules right a Hacker can replace the Captain or Exo (or anyone) with whomever he wants once.
How about this to keep our Captain honest: if he doesn’t have a good candidate by the end of the Day to arrest or release, he should put out an arrest warrant for himself. The Chief then can brig the Captain if needed.
I don’t think I like it though since outstanding warrants give the mutineers more options to reach their win condition (get someone as Chief, brig a town with outstanding warrant).