There is an episode near the end of season 6 which me and many fans of a certain character find downright insulting due to the unnecessary character destruction which takes place in that episode.
Given that the Doctor married with a flesh-and-blood human in what we see of that future, I'd be tempted to answer the 2nd question with an admittedly highly tentative 'yes'. At least, he wasn't reassigned to the dilithium mines or simply reset to factory parameters.
Ok, Fury then. I made the decision to skip that one. I was referring to "Unimatrix Zero" and "Nightingale", where the writers decided that it wasn't enough to make a certain incredibly stupid decision regarding one of the characters; they decided to rub our collective nose in it.
Course: Oblivion hands down. Talk about having the existential rug pulled out from under you. And their faces were falling off!