They're really doing this less than a year after he takes command? It's disappointing.
Actually it kinda makes sense. If someone were given command of the flagship right out of the Academy, no matter how heroic the circumstances, there'd be a lot of questions about his qualifications and a lot of second-guessing. It stands to reason that Starfleet Command would be watching him closely and ready to take his command away as soon as he screwed up. So this version of Kirk at this early stage would be far more likely to have his command revoked than the more seasoned Kirk of the Prime universe.