There is no degrees in cheating or hacking and changing the program. If you do it you're just as guilty as anyone else who does it. If there is honor in PrimeKirk's actions, there was honor in NuKirk's. If there is dishonor in NuKirk's actions, there is dishonor in PrimeKirk's.
These gyrations to make it seem like there are degrees to cheating in order to make PrimeKirk look good and NuKirk look like an insult to the character Kirk are going to hurt someone's neck.
That makes no sense. We never got to see how Prime Kirk actually performed the test.
Really, the analogy here is an arcade videogame. You can apply a cheat that makes your guy invulnerable, OR you can remove the cheap-shots that those games throw in to prevent you from getting through on one quarter. If you do the former, you can play the game without even thinking. If you do the latter, then you still have the be the best there is at playing it to get to the ending. My feeling is Kirk did the LATTER, and that's why he got a commendation. He still earned his stripes based on his sense of what the test was supposed to represent.
It doesn't matter that officers are supposed to lose. If Starfleet is interested in competent officers, it is going to be impressed by prime Kirk's legitimate performance on the altered test. His intention wasn't to
cheat. His intention was to fix what he felt was a rigged test so that he could
EARN his stripes fair and square. Two different things. If anything, this showed that he was more about principle than blindly following the rules.
Again, Kirk made it possible to win, not a cakewalk. It could have been the equivalent of changing one parameter that slowed things down enough to allow for the latency of human reaction-time. Anyone who has played a lot of videogames knows that they must be carefully tuned to the limits of human physical hand/eye coordination. You want the difficulty hard enough to seem impossible to the novice, but not so hard that it is physically impossible to beat. The best games of all time fall under that category of requiring exceptional skill, but are not completely unbeatable.
The existential question posed by this is that in life, there ARE no win scenarios, and that even a seasoned officer like Kirk could face them. The sin of hacking the simulation was not against Starfleet, but against himself, because he held onto the idea that he could somehow escape death every time. Rhetorically he knew the moral of the test, since he schooled Saavik about it, but he had never experienced a situation he couldn't somehow weasel himself out of (like in the Corbomite Maneuver). This is the foreshadowing that sets things up. The audience is asked to accept that maybe Khan represents the no-win scenario and that no innovative thinking on Kirk's part will be enough to save them, which is in effect true, hence Spock makes the ultimate act of sacrifice, leading to his poignant line "I never took the Kobayashi test until now. What do you think of my solution?"
This is the thematic bedrock of the entire picture and JJ merely used it as a form of mild comic relief and pseudo-fan-service.
In his mind, he feels like he's reciting Trek gospel, but it's a real mis-read of the character, because he just doesn't get Trek.