I think in an earlier scene we see engineering staff wear suits but I'm not sure (I really need to see this movie again). But you're right that in TWOK Spock doesn't bother with a suit, either, he just takes a mask and gloves. I always took it to mean that it wouldn't have mattered, anyway. Scotty would have sent someone in or gone himself if a suit had been protection enough to survive.
But getting back to where this all started, Kirk is promoted from cadet to Captain against all common sense, in ST:09. Then demoted at the start of this film cause he's clearly not ready. But at the end of ST:ID, he was again in command. But in everything I've read, no where do I see he understands and accepts what he did was wrong. He simply gets rewarded for saving the day again.
He becomes Captain again halfway through the movie because Pike dies and Admiral Marcus sends him on the mission to kill Harrison/Khan, not because he saved the day.
What he did on Nibiru was against regulations and against the Prime Directive but was it morally wrong? After all, he saved a civilisation from extinction and the presence of the Enterprise was only revealed because he chose to save Spock instead of letting him die. That's very Kirk, I'd say. We saw Kirk go against the Prime Directive (as it was later interpreted, anyway) quite a couple of times in TOS.
As for self-reflection there is a poignant short scene between Kirk and Spock where Kirk explains his way of doing things and that he actually doesn't know what he's doing. Both Kirk and Spock have character arcs that I thought were interesting. So it's not like Kirk is staying the same throughout the movie.