It's walked a fine line throughout the series between being snooty at policing-by-violence and glorifying it. Sam is usually in the right though : if he says "no, this guy didn't do it", he didn't. And note that right up to the ending credits, Sam is expressing his disapproval of Hunt's actions...

I think his decision comes down just to Annie; his promise, and that, as they say "you can never go home again" - i think the remoteness and emptiness is a symptom of that. It's very significant that the scenes after he woke up from coma had a very subdued soundtrack, almost silent.

It reminds me a bit of Alan Moore's spin on the Alice adventures in The League of Extraordinary Gentlement, where, having returned from the Looking-Glass she has had her chirality swapped and can no longer digest food.