Exactly - and that is why he went to Scotty in the first place, to accuse him of everything that was not going smoothly with the impossible assignment. It's the classic "leadership by arrogance" approach that Kirk practices throughout the movie (even though the writers try to convey that he would be practicing it only for the first half).
I'd agree with this except that leadership by arrogance really isn't leadership at all. Kirk took the Enterprise
away from Decker merely because he wanted
it in spite of not having spent so much as five minutes aboard the vessel (or so we're lead to believe) during it's eighteen months in drydock. He had no idea about the modifications to the ship's engines or its weapons array (phaser intensity improved by using warp power), nor did he understand why the transporter system wasn't functioning properly (hence his accusatory question to Scotty). Decker not only knew these things, but he also had a hand in tracking down and fixing some of the problems in question (he found the faulty sensor associated with the transporter while repairing a computer console in the engine room).
Kirk was fortunate that so many of his senior staff were still serving aboard the ship, or he'd likely have faced a mutiny over his boneheaded decisions. Even so, it's amazing that only Decker (and to lesser extent Scott and McCoy) call him out for his unfamiliarity with the refitted vessel.
And as usual, Spock was left to clean up after him by helping Scotty correct the warp engine imbalance, something of a small miracle given that Spock hadn't been on the ship, either. Then again, Spock did say he'd been studying the Enterprise engine design and was aware of their difficulties. This suggests he'd tracked down the problem himself and was prepared to help Scotty fix whatever was wrong.
Christopher does a nice job following up on some of these issues in Ex Machina
by depicting Scotty nursing something of a grudge against Kirk for pushing Decker aside. Their confrontation over Scotty's alleged "perfectionist jag" is one of my favorite parts of the novel. Moreover, the rest of the crew seems split on whether they want to accept the return of the Old Guard (Kirk, Spock, McCoy) after the new group (Decker, Sonak, Chappel) was swept aside so easily because Kirk wanted it that way. Of course, we'll never know what might have happened had Sonak lived and Spock had still tried to board Enterprise
while en route to V'Ger. Would Kirk have pushed the younger Vulcan aside in favor of his best friend?
Granted, Kirk wanted Enterprise back.
But if there hadn't been an emergency, with this particular ship the only one in range, would he have muscled his way onto the bridge? Maybe, maybe not.
Kirk saw himself as the best option to lead this particular crew into this particular situation. Wanting his ship back was in the back of his mind and did influence his initial attitude, but his instincts turned out to be correct.
It doesn't matter who was already assigned to the crew. Once he took command it was his call to place who he thought were the best people in those jobs. It happens in the real world all the time, like it or not. The boss calls the shots.
Not having a working knowledge of the ship's redesigned systems is at most inconsequential. It happens in real world situations daily. Decker's countermanding of the phaser order was correct, and Kirk acknowledged that. Kirk was wrong to assume that Decker was competing with him in that instance, and his defensiveness was wrong. He acknowledged that. McCoy asked to accompany the two to Kirk's quarters because he saw what was coming. Bones acted to reign in Kirk's, for lack of a better word, "enthusiasm."
Having a legendary captain on the bridge would not have inspired mutiny. Everyone on board was surely familiar with the missions of the Enterprise under Kirk's command.
Kirk's competence should only inspire confidence in the crew. His confidence in his capability as a commander might cause others to see that as arrogance, but as they say, "it ain't bragging if you can do it."
Placing his trusted confidants in positions close to him should not be seen as a slight to any crewmembers who might have been displaced. They are professionals, there to do a job. Personal feelings have to be put aside. Yes, even Decker.
As Uhura said, paraphrasing, "Our chances of returning from this mission in one piece may have just doubled."