He directly defied the commander-in-chief of Starfleet
(the one charge that stuck) - and turned out to be right to do so. If he hadn't gone, Starfleet would have no clue what went wrong with either the Grissom
or Genesis itself - and next thing they would know the Klingons would be lobbing Genesis-derived torpedoes at Federation worlds. But doing what he did is not
how a Navy is supposed to be run, on sea or in space. By being rendered unable to discipline Kirk in any real way, and by being proven wrong by him, Starfleet Command has egg on its uniform.
Rubbing salt into the wound, this same rulebreaking guy was Starfleet's golden boy only a dozen or so years earlier. And in the public's eyes, Kirk is still
the galaxy's biggest hero - which means the other Admirals, and everyone else in Starfleet, are being unfairly measured up against him. And found wanting.
Thus the image of Kirk in SFC's eyes becomes that of a rogue past-his-prime 'cowboy' who, while still useful when the chips are really down, presents exactly
the wrong kind of role model for young up-and-coming officers. They'd start to defy Starfleet Command on a regular basis and pull crazy stunts too. Yes, Kirk was usually right whenever he did - but in this line of work, you've only gotta be wrong once. So keep him busy for now, but start looking for the first opportunity to get him off the payroll for good.
Trying to steer this back on topic, giving him a 'lemon' was perhaps SFC's way of reminding him his being broken down to Captain was supposed to be a punishment as much as a reward. And yeah, perhaps the Nimbus assignment was Starfleet setting Kirk up to fail.