This is actually a pretty plausible theory when certain facts are taken into consideration.
Skipping over the idea that Stevens himself was involved in gun running to Syria, there are a couple of points that fit into the overall scheme that Glenn is trying to go with.
1. There was a CIA safe house in the consulate in Benghazi. We know this because it was leaked during the investigation of What Really Happened in Congress.
2. The Syrian branch of the Muslim Brotherhood is a comparatively secular organization. Their charter doesn't even mention Islam, and they have stated that they are interested in a secular govt to replace the Assad regime.
3. Islamic groups are notorious for fighting amongst themselves and infamous for their attempts to radicalize secular Middle Eastern political organizations.
4. Given point 2 and 3, it makes sense that an Islamist militia would try to disrupt gun running to a secular organization in Syria.
This definitely has more meat than Beck's usual nonsense (ie: Rockefeller center is an homage to Communists).