If I remember correctly, the guy was beaten to death while refusing to give a false confession and the FBI agent was given some sort of tame "reprimand" I seem to remember the agent being named at one point but it is apparently not in the wiki article right now.
http://en.wikipedia.org/wiki/Kenneth_Michael_Trentadue According to Wikipedia, which others tell me is strongly supported by a cadre of both state and federal court workers, there was more than one "suspicious suicide" related to Trentadue's death. A witness whose testimony was verified by the FBI investigators was then also found hanging in his cell of apparent suicide.
The FBI is really the top of the food chain with the Bureau of Prisons but clearly whatever was done in that, the BOP is ultimately responsible for carrying out the murder and coverup, as it took place on their turf and under their control, but like loyal servants to evil, they are apparently not giving up the names of the order-givers. Could well be an FBI agent delivered the death blow personally, as one account I read involved the guy refusing to sign a false confession once he figured out he had been fatally wounded and was not leaving BOP custody alive, and the fed lost his temper and finished him off slowly with no further attempts at gaining a confession.
One way to test for prolonged torture however is a toxicology test on the subject. Professional torturers will administer certain strong narcotics in order to keep the subject alive and in pain during the torture sessions, but if the person "breaks", then they get an overdose of painkillers or at least a shot of morphine as they bleed out. If no drugs are found, they likely went out hard core. If exotic substances are found, then it is an indicator of a more sophisticated and prolonged torture program.
Responsibility for death is also fairly well established in international legal circles if a person commits suicide in custody as a result of not being willing to withstand further torture.