A successful evacuation would set a precedent, and that's all that would be needed to turn the Federation into a Galactic Nanny State once a skilled rhetorician said that the evacuation was a key example of how Starfleet should react to all planets in danger. As a result the fleet would have to actively search out all endangered worlds and constantly repeat Boraal no matter how many resources it would take to do so, draining the Fleet's numbers and the Federation's resources.
The Federation exists in a state of abundance. They have billions of citizens, hundreds of worlds, and thousands of ships. They could handle it -- and that's assuming that everyone is as much of an extremist as to require that the UFP specifically seek out distant, endangered worlds far beyond its borders rather than simply requiring Starfleet to make heroic efforts to save civilizations located near or even within Federation space from extinction if so threatened. (To be fair, your argument would carry much more weight in the Federation that exists post-2381 in the novels, [spoiler="Star Trek: Destiny" and other novels]which has been absolutely devastated by the Borg invasion[/spoiler].)
In any event, I never cared for the way the TNG-era shows interpreted the PD. Instead of being a bulwark against imperialism, it became another
tool of imperialism -- treating less technologically-advanced societies as though they were inferior to the UFP rather than as equals, and using the excuse of their supposed inferiority to enforce Federation technological dominance over its neighbors before, if INS is any indication, immediately inducting them into Federation Membership before they've had a chance to establish themselves on the interstellar stage as the Federation's equals. Oh, and if you haven't passed an arbitrary standard in technological development, we'll let you all die. It's basically passive imperialism rather than active imperialism.
I think that a story featuring the Prime Directive would be much more interesting if it were to be applied to situations akin to what we find today. For instance, the Sudanese government and government-backed militias have been engaging in a genocide in Darfur for years now. Under one conception of a Prime Directive-POV, the United States should not intervene (and, indeed, that is what has happened). On the other hand, the U.S. and its allies
did intervene to stop a genocide in Kosovo. Was that right? Wrong? Look at the situation in Iran today. Under an anti-imperialist POV, should the U.S. intervene?
Many cultures in Africa practice female genital mutilation, which can be positively deadly if performed in unsanitary conditions; as a result, some Westerners want to teach people how to perform these acts in sanitary conditions to reduce deaths from infection. Others argue that that's essentially the same thing as becoming an accessory to assault and mutilation, and that we should either try to persuade these cultures to abandon the practice or do nothing at all about it. Some argue that those cultures have a right to follow their own practices, but some argue that if we accept the idea of universal human rights, this means that there are some things that no culture has a right to do to anyone, diversity be damned. Who's right? Who's wrong?
Similar situations would make for fascinating PD stories -- instead of dealing with the interstellar equivalent of the Primitive Tribal Savages Who Are Clearly Too Foolish To Deal With Our Clearly Superior Civilization And Technology (an archetype often used by Europeans to
justify imperialism), let's see situations where cultures that are clearly technologically and intellectually comparable to the UFP doing things like committing genocides. Should the Federation intervene? What if there's a democratic movement trying to overthrow a tyrannical dictatorship on their homeworld and they're asking the Federation for aide? Does the Prime Directive stop the Federation from having diplomatic relations with governments waging civil wars, or with governments that practice de facto slavery over a majority of its citizenry? Should it? How do the Klingons feel about the fact that their last two Chancellors were installed by Starfleet officers -- was that legal under the PD? How do most Ferengi feel about the fact that their last two Grand Nagi were clearly so influenced by Federation cultural values that they instituted wholesale revolutions in gender relations and business practices -- was
that a PD issue? If, say, Orion or Klingon culture requires the ritualistic mutilation of the bodies of, let's say, little boys, should the Federation get involved in trying to stop that? Or trying to at least prevent deaths from infection?
These sorts of conflicts and dilemmas would be much more realistic, and much less condescending, than the "OMG we can't let the primitive natives see us or use our radios!" nonsense we've gotten before.