As far as I understand it there is no evidence that Chris Stevens was raped, and that his death was likely due to smoke inhalation from the fires.

In his death picture his hair appears perfectly coiffed, his shirt was off, suggesting he took off his shirt to breathe through it hoping to filter out the smoke before his death, also his pants were not off and fully buckled in.

Supposedly they dragged him out of the building and took him to a hospital and that he had no other injuries apparent.