I tend to think it was less breaking the rules than it was lying about it that got Kirk in trouble. Rightly so. Had Kirk manned up to it, he probably would have gotten off with a lecture. Instead he proved that he wasn't a man, but a teenage boy who feels no responsibility to anyone or anything. The events of the previous movie were probably the difference between being demoted and being kicked out completely.
This of course assumes Prime Kirk didn't lie in his reports everytime he broke the Prime Directive.