If I may respectfully offer a notion:
I think it's sort of a notion that a planet must develop so far on its own, before a more advanced culture comes in to offer that planet aid.
In the case of the Nibiru, Pike refers to their culture as having barely gotten past inventing the wheel. And as the audience (and the crew) saw, they are a very primitive, spiritual, and perhaps even superstitious people.
The Vulcans largely ignored Earth until Zephram Cochrane was able to invent warp drive for it. And then, for those who take Enterprise as canon, the Vulcans still did not present everything on a silver platter.
Imagine what could happen if the Vulcans just gave all knowledge to Earth all at once. That would be a lot to process, for starters. And then, what about the various cultures of Earth that might still cling to older beliefs? How would such a radical change affect them, and their place in the larger world-view?
Now, imagine just waltzing in and saving a primitive, spiritual, superstitious people (Nibiru) from potential world ending disaster...and they become aware of it? Everything they've ever known or held to be true would seem like one great big lie to them...and then it could just spiral from there. It could potentially lead to a fate worse than if they'd been destroyed by the suoervolcano itself.
The Nibiru saw the Enterprise rise from their ocean, fly into the mouth of the still-firebeast, soothed its raging bellows, and then flew off into the great whereever. We saw that one among them was drawing a not too shabby image of their savior into the mother sand. The high priest dropped his holy scriptures as if it were nothing more than a dirty tabloid, and started bowing before it. Everything those people knew, up to that point, suddenly became a lie for them, it would seem...and they started bowing before a new tin god.
Then, on top of all that, what if the Federation comes back and tells these now confused souls that "there are no gods"? (actually, the Feds wouldn't as they respect the right.of spirituality among its citizens and protectorates)....but what if they did?
The Federation has come to the conclusion that species must learn some things on their own before the Feds come in to offer advanced guiadance to a larger world, lest that culture potentially destroy itself with trying to use knowledge beyond their understanding.
What Kirk did was morally praiseworthy, and right. Unfortunately, it was not right in the spirit and letter of the law.
Much the same as someone terminating a serial killer without the due process of law afforded to the serial killer that is supposed to be afforded to every criminal/suspect. It might be morally praiseworthy and right....and even get that person branded a hero in some circles....but unfortunately (oft, to our chagrin), it is still legally wrong.
At least, that's my view on the matter...and as always, it is simply my opinion.
