Having a gay ambassador in a Muslim country IS an issue. It puts him in added danger in a variety of ways, even if he did remain celibate...which is unlikely. His rape was not only a disrespect to him personally, but also a message to our government...who surely know the truth of this no matter what they say.
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.