The fact that severe isolation serves an additional purpose beyond simple punitiveness, such as minimizing the risk to prison staff posed by extremely dangerous inmates, doesn't contravene the idea that severe isolation is a form of torture any more than waterboarding for the purpose of interrogation does. But as a culture, we're very used to the idea of extreme isolation in punitive settings, we're so used to thoughtlessly dishing out punishment without regard for the attendant social consequences because the human beings we throw in prison are so meaningless to us as a society that we don't think very deeply about it. Of course what makes the conditions of Manning's imprisonment even more disconcerting is that he's being punished without having actually been convicted of anything.
Manning is a less than sympathetic figure. But month after month of solitary confinement and deprivation well beyond what we give convicts on death row strikes me as cruel and inhuman punishment. And Manning merely stands accused of crimes.