Hacking the program is wrong either way, but that's not the point. Hacking the program is all nuKirk did. What PrimeKirk did was not use a copy of the test answers-- he added his own option to a multiple-choice test. They offered him A and B and he came up with C. That showed them his potential.
How do you know this? All Kirk says is:
KIRK: I reprogrammed the simulation so it was possible to rescue the ship.
DAVID: He cheated!
KIRK: I changed the conditions of the test. I got a commendation for original thinking. ...I don't like to lose.
Nothing in that exchange tells us what he did.
The later scene were he lowers the Reliant's shields is homaged in Kirk lowering the Klingons' shields in ST09. The writers chose that for a reason, just as they included the apple eating scene.
Adding your own answer to the test and then using that answer when taking the test is cheating.