At the time, he was working under the Secretary of State. He was under orders from Hillary.
He was working with the secret CIA scheme
As long as everyone understands that it wasn't the CIA. It was the Department of State's Central Intelligence Unit (Agency).
... of buying old Libyan SA-7s and other weapons and shipping them from Benghazi to Al Qeida and ISIS through Turkey.
Hillary had HER CIA buying the weapons from the rebels (aka 'citizens') at a discount. Then she was supposed to sell them to the terrorist groups that Obama is supporting. She stiffed them and offered to sell them to a different group of rebels for more money. The first group was reasonably angry and took revenge.
He and the Benghazi office were ARMING Al Qeida.
In this case, they didn't, because Hillary skunked the deal. (although arrangements were made later to get those weapons to them). That is why Obama wouldn't let the Military go rescue the Ambassador and the Special Forces and the State Intelligence Agents. She was trying to rip everyone off for the cash and so Obama just ignored it and figured it would all be blamed on Hillary. He couldn't outright say so because it would show his involvement in supporting our enemies.
I think you are kinda lost. The CIA isn’t under State. And the CIA has been enthusiastically supporting the Syrian jihadis and was instrumental in their equipping and arming.
Our entire government corrupted itself out over Libya and switching sides to Al Qeida. The refusal to give fire support and tell the truth is because it was a highly covert CIA/State joint op.
The CIA wasn’t some victim of State. They were all cooperating and were horny for war in Syria.