I don't think the sequence was supposed to show the whole thing about the Prime Directive (the boundaries of which seem to depend on the plot requirements of the story).
It was intended to show that Kirk HAD been promoted too quickly in the '09 movie. Pike calls him out on it, telling Kirk he's bending the rules constantly indicating this isn't the first time. Kirk even argues that the rules don't apply to him.
Then his whole world is torn from him, and Pike wanted him as First Officer in order to give Kirk the guidance to become the Captain he should be. Admiral Marcus was probably counting on the fact that Kirk's career was on the line, thinking that Kirk would just follow the orders to launch the torpedoes following his humiliation and dressing down.