One of the things that bugged me (mildly) about Star Trek: Into Darkness was its decision to be consistent not with the original show's version of the Prime Directive, but with the one established in The Next Generation and beaten to death in Voyager.
The Prime Directive was there in original Trek. It got referred to on a regular basis. But Kirk and Spock and McCoy broke it all the time. And the fact that they broke it all the time and got away with it can only be attributed to one thing: the original Prime Directive was a regulation intended to promote moral outcomes. It was designed to protect developing civilizations, to allow them the freedom to grow as they naturally should. When the crew of the Enterprise acted in accordance with that purpose, their superiors let them get away with breaking the letter of the law if that was the only way to adhere to its spirit.
But in the later shows, and in Into Darkness, the Prime Directive has been elevated to a moral good in and of itself, while simultaneously decaying into a cowardly piece of CYA bureaucratism. Latter-day Trek forgets the protective intent of the original, choosing to view nonintervention as an absolute moral stricture -- even when nonintervention guarantees that instead of being protected, a developing civilization will instead be destroyed. Nonintervention has gone from a tool for avoiding harm to a dogma that needs no purpose or goal, that must be followed because it is presumptively good, regardless of what evil might result from its application. And when a justification of this attitude is required, the one that is implicitly communicated is this: "If we do nothing, we can't be blamed for screwing things up."
Note to the clueless: it is not morally defensible to allow an entire civilization to be destroyed by a planetary cataclysm just because you're worried that saving them might result in their civilization being altered from its pre-cataclysmic state!
Ultimately, Star Trek is about being the good guys, and the Federation is supposed to embody that. The notion that entire civilizations should be allowed to die, simply because they have not yet developed warp drive, makes a mockery of the Federation's core morality.
Into Darkness isn't quite as bad about this as some episodes of Next Generation and Voyager were: the thing that really gets Kirk in trouble is not saving the alien race, but choosing to allow the Enterprise to be spotted in order to save Spock. So there's hope that future installments in the franchise will be truer to the TOS Prime Directive than TNG's or Voyager's.
I certainly hope so. The last thing we need is more Star Trek built around dogma instead of reason.
Shouldn't the real Prime Directive be: Use your brain!