This, however, was an extraordinary circumstance. How many 3rd year cadets do you know who saves the entire (in this case) planet and billions more lives from certain and imminent destruction? Who shows exceptional leadership and tactical knowledge that is superior to even the most up to date military leaders? Also, Kirk was given the rank of First Officer on that ship by Captain Pike.
Then again, it's apparent that Starfleet isn't quite a military organization according to Captain Pike. It holds similarities, but there are differences. This is apparently one of them. And one more thing: We're looking at least 200+ years into the future here. Things are bound to change a bit in such a culture, particularly one as broad and varied as this one. Kirk didn't just save Earth, he saved the entire Federation and billions, if not trillions, of lives.
J.