I'd like to reemphasize that we don't even know what Prime Kirk did.
For all we know, nuKirk was "just as commendable as PrimeKirk" but it was Starfleet's attitude that was different. Starfleet was under greater pressure in the nu-timeline, due to the Narada incursion. Perhaps the brass was grimmer and took a dimmer view to cheating.
And, I really think that the Enterprise was gimped in the Prime Universe simulation. The test seemed overtly unfair. Doing something unfair to counter inherent unfairness seems like fair play to me.
Also, a commendation for original thinking sounds like a begrudgingly made compliment, if not a backhanded one. Perhaps command wasn't so much praising what he did (altering the test) as why he did it (never give up, never surrender).
Another point that just occurred to me. Using the prefix code to order Reliant to lower her shields sounds exactly like what nuKirk did in the simulation: nuKirk eliminated the Klingon shields. If Klingon ships use a system similar to the Federation ships, then the prefix codes of Klingon ships would be all that would be needed to eliminate Klingon shields, out of simulation. Is spying really cheating, in war?
If what Prime Kirk did to save the Enterprise from the Reliant in their first engagement was good, then why would it be utterly bad for nuKirk to use the same principle in the simulation?
But again, it wasn't an unfair test, the test wasn't about winning, it was about testing your metal in a hopeless situation. Yea, it's a mean thing to do, but, they consider it necessary to see how you react under those circumstances, in order to help weed out your Commodore Deckers. It's only unfair if you consider the reason for the test is to test your ability to win against it. I'm sure today's military pulls the same kind of thing (Letting you believe a test or training scenario is one thing, but, it's really something else. In fact, I would be surprised if they don't engage in their own Kobiyashi Maru tests at some level of Rank advancement), and I wouldn't be surprised if there are many College classes that also give you tests or puzzles you think are one thing, but, they're really something else.
Kirk's metal
was tested. He didn't like having loss forced down his throat, so he changed the test.
That was how his character reacted. Kirk's point was that it is a poor character trait to just roll over and die. He wasn't going to stand for a test that could not be beaten.
If you
really think the test wasn't unfair, then you must think that neither nuKirk
nor Prime Kirk deserved to be commended for altering the test, because in that case, by altering the
fair test, Kirk failed to get the point of it.