I don't know enough about this person to say one way or another whether he was a high ranking al qaeda member or not. But _even if he were_ I don't think insisting on a habeas corpus rights for detainees or decrying torture is a _damaging_ thing at all. It was up to the state; who originally imprisoned him and almost certainly tortured him to prove his guilt. They didn't even attempt to do this; and it likely had nothing to do with not wanting to reveal intel -- the 'court' he'd have been charged in had little to no due process, and the evidence was presented to a government tribunal, not to the defendant.
I think Smiths point there wasn't that there was some problem-meanness correlation, but that the justice system as it is structured doesn't even try to have a sensible metric by which to sentence by. I think framing it in terms of damage done to society is a reasonable one. Under such a metric, (unarmed) robbery should be treated with much less severity -- and daresay rehabilitative measures as opposed to just imprisonment -- than rape or murder. That seems reasonable, and not particularly evil as worldviews go.