It's not a wild claim at all, it's been substantiated by the contents of secret diplomatic cables published by WikiLeaks.
You believe Kopassus has been cleaned up? You must be joking. Yudhoyono committed to any soldiers convicted of human rights abuses being expelled from the military. The three soldiers who comitted torture in West Papua were not convicted of human rights abuses and were not expelled.
The torture included "kicking one of the men, Tunaliwor Kiwo, in the face and chest, burning his face with a cigarette, and applying burning wood to his penis. The soldiers placed a knife to the neck of the other man, Telangga Gire, while threatening to kill him. Kiwo later described in a videotaped interview how the torture went on for three days. The soldiers beat him with their hands and sticks, crushed his toes with pliers, suffocated him with plastic bags, burnt his genitals and other body parts, cut his face and head and smeared the wounds with chilies."
Opinion: Indonesian military gets away with torture | Human Rights Watch