I think you're giving him too little credit. She wouldn't have been able to convince him so easily if he was that blindly obedient. The whole reason he put this unconventional team together is because he's able to think outside the box.
Really? Because I have not been seeing that, at all.
It was questioned in the first episode when they brought Skye on board; I saw it touched on in the Malta episode which concluded with this utterly dangerous device must not be destroyed and is only safe in SHIELD's custody, and the "Skye betrayed us" episode - which concluded by stating Skye was absolutely totally in the wrong and she should be ashamed of herself for failing to betray her principles and a longtime friend and lover to her new team-mates, and how dare form any loyalties to others before she met the team. That's, what, 3 episodes out of how many?
Given that you had no trouble listing several examples, it's rather hyperbolic to claim you haven't seen it "at all." And you're misrepresenting at least one example. You're forgetting that Coulson insisted that the gravitonium be stored without any record; he listened to Hall's concerns about this power falling into government hands, and therefore he hid it away where SHIELD wouldn't know of its presence, and he didn't notify them that it was there. He deliberately deceived his own superiors because he didn't trust them enough to let this power fall into their hands. Maybe you need to watch the episode again, because you clearly missed some crucial details.
And "0-8-4" was also about the potential abuse of power, because it was about a former ally of Coulson's betraying him due to the temptation posed by a Tesseract-powered weapon. So I'd say the theme has been an element in at least half of the eight episodes to date. Which is not an atypical concentration for arc elements in the early part of a television season, since such elements are usually fed in gradually, especially in a premiere season.
Again -- it's early yet. I'm sure it will be more prominent later. As I said, we know it's going to be a major thread in the next Captain America movie, which is very SHIELD-centric and which will come out during the latter half of the show's first season. It seems quite possible that the show will build up to that movie's events and then deal with their ramifications to the organization.