He jumped up the ladder, got command of the Enterprise, and was basically acting like he could do no wrong.
So Kirk was acting like a typical Starfleet captain basically.
Stopping a bad guy doesn't say anything about his command abilities. An incident where he violates the a major directive, doesn't care and even lies about it, does.
So the problem here is basically that he's James T. Kirk.
Or are you seriously going to tell me that Kirk never broke the rules.
As for the lying in a report thing, didn't Janeway once make it sound like Kirk had a habit of fudging the details in his reports.