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Before knowing what to do with Graner, I think we'd have to find out to what degree the Stanford Prison Experiment type situation influenced him. If he was being put in a situation where virtually nobody else could have resisted either, then he should be put in intense therapy (especially as he evidently has had PTSD for a couple decades) and his superiors jailed.
Under the current circumstances, not only should everybody involved be tried at the appropriate level, but we should ensure the same standards of handling/punishment are applied to all prisoners. Either we discipline severely on tiny offenses and have that be part of the jail's code (or sentence), or we don't -- it shouldn't be up to individual prison guards.
Personally, though, I still believe what I was taught as a child: the hallmark of an advanced civilization is making decisions from rational, logical thought, and not letting base emotions be in control. The "eye for an eye" attitude belongs to societies (or subcultures in the US) that most people in ours have little respect for; we need to think carefully before deciding who to emulate.