The only version of that story I've seen was from a Lebanese news story in Arabic, which claimed that Stevens got the same treatment as Gaddafi. I suspect it's just the bad guys trying to claim credit for more evil than they actually accomplished.
More reliable reports are that Libyan friendlies transported Stevens suffering from smoke inhalation from the burning consulate to the Benghazi Medical Center, where he died. Reportedly, the Libyan doctors worked on him for 90 minutes before giving up. They also reported he had no injuries inconsistent with smoke inhalation. Stevens had been scheduled to meet with some of those same doctors the next morning in order to hook them up with American doctors eager to help them improve the BMC's operation.
There is a video of the Libyans carrying the ambassador. The don’t look so friendly to me. The idea that attackers looted the embassy then atacked the safe house and then just walked away leaving the ambassador behind is of believable. The usual MO of rape and torture is more likely.