The difference, in this case, is that not only were arms being sold to a hostile entity, but they were also being funneled to one (hostile to the US).
The government rushed to support the Islamists, or rather the “rebels,” even though it must have been known that many of them were AQ, since I recall this being discussed from the very start.
I don’t think this bothers Obama at all and is consistent with his policy of arming Islamists, but I think there are still at least some people in the government who don’t accept this and they were probably the ones trying to retrieve the weapons. But Obama (a) probably didn’t support that effort to begin with and (b) didn’t want the truth to come out about his rash and dangerous support for the “Arab Spring” Islamists.
They could, they can: but on the ground in Benghazi on September 11, U.S. foreign policy was not the issue, American lives were. This indeed was "a moment to choose sides." In the battle between good and evil, the hymn says: in this moment, the administration was not being asked to choose between good and evil on the global scale. If they do not want to see evil where it is in the global picture, okay, that is why we have elections periodically. This was a case of evil in a small place, involving a desperate fight between good men and evil savages. They, the administration, did not choose or, God help us all, they chose the wrong side."
Sounds like a valid reason for the administration to want our ambassador dead. He simply knew too much. Therefore, no backup during the raid on our consulate. The only real question is who in the administration knew about the attack before it happened. When we have a president that kills Americans with only a star chamber trial, all things are possible.