Among the SHIELD agents present, Phil was a level-six with the highest authority, while Sitwell was only a level-four.
Also, Phil was the person in charge of this mission, so Sitwell could only be considered a subordinate.
The bald agent, Sitwell, wasn't actually brain-damaged.
It had been his plan from the beginning to cause trouble. He had thus brought a group of agents down here to court death, so that SHIELD would provoke these powerful aliens. It then wouldn't be easy to resolve the ensuing blood feud.
Also, this would frustrate Phil's efforts and hinder Nick Fury's progress.
But now that everything had quieted down, Sitwell could no longer stir up trouble.
If he acted too overtly, Phil would definitely have him investigated by Internal Affairs when they went back, which would hold Sitwell back from doing a lot of things.
