The writer of the fic linked above seems to totally share my mind. Not the Michael/Dean interaction but ...
I've been thinking (probably more than it deserves) about Ana's "All the pain, twice the self-righteousness". (And: quoting from memory.)
And there is a way to reconcile it with getting Dean to torture Alister. The point of that was not that Dean was the only one with the skills (though I'm sure Castiel sincerely believed that.) And it was not just Uriel's little plan for Alister to kill Dean, though I'm sure that was sincere too. What it did to Dean was the point; someone higher up that both Uriel and Castiel intended to make sure Dean stayed broken, had his face rubbed in his time in hell now that he was out. So hell really did learn its torture techniques from heaven. Not canon, but not inconsistent with canon.
Also, (and here again the fic deals with something I've though before) the timing on Dean's rescue is suspicious. No one notices when he goes under that he has the bloodline hell needs to unleash apocalypse. Especially no one notices when unleashing the apocalypse is something heaven and hell agree on. They were sick of haggling over a few souls at a time during the pregame, and wanted to start the big game (which they now seem to have done). That is how they just notice how well Dean fit into prophecy only after he broke and rescued him too late. No accident, Dean's breaking was part of the plan.
And maybe the writers won't go that direction. But it would not be at all inconsistent with the direction they seem to be going.