I think this might be Renegade Atlas (http://archiveofourown.org/works/569056/chapters/1018777) by pumpkinless. It's also in ff.n however, I don't know the link there. The author did repost it in AO3 and mentioned that it was in ff.n :D The torture of the Sam look-a-like happens really early.

Anyway, if you're looking for stuff like this (Castiel being tortured by Dean in a Destiel setting) then also try The Forty-first Year (http://archiveofourown.org/works/68628) by tracy_loo_who and Bones (http://archiveofourown.org/works/259039)by apokteino.

:D