How is it military protocol to question an emergency evacuation order? In a crisis situation like that, protocol requires that all hands pitch in and do their duty to facilitate the evacuation, rather than delaying the commanding officer with useless objections. Fury's decisions weren't "faith-based" at all. He was moving personnel out of a facility that was in imminent danger of implosion, had a team working to avert said implosion and also had the presence of mind to order the removal of important materiel. All of those were very practical actions dictated by the circumstances they were facing. The entire operation was very orderly, if rushed. In ordering Hill to see to the Phase Two prototypes, Fury was ensuring that a project the WSC valued more than the Avengers wasn't destroyed with that base. Had he failed to secure the prototypes, it's a pretty sure bet that his superiors on the Council would have attacked him for it, fed the details by Hill, who was reporting on Fury's every alleged lapse in judgement. Fury did not agree with Hill's point about the tesseract or anything else, he merely did what he would have done had she not said anything. He was marching down into the bowels of the facility, where the cube was being held, even as she followed along talking to him. Fury sent Hill off to where she could be put to use caring for the Council's toys and went to check on Selvig as he had intended. When I referred to Hill undermining Fury, I meant far more than her wanting to await the tesseract's implosion with her thumb up her ass. In the deleted scenes, which I consider canon, it was made very clear that Hill was giving the Council negative reports on Fury and SHIELD, with special emphasis on the "freaks" he was assembling. The Council was after Fury's job and Hill was more than happy to give them ammunition to use against him. In one of the scenes she had told them that Hawkeye was compromised, making sure to emphasize that he was an assassin. A member of the council pointed out that Hill had been giving them negative reports on Fury for some time before the events of the film. It turned out that Fury had been right about everything all along, of course.