Well, I think it's lost on people and we, as the Federation, shouldn't even be asking them to leave. That's the "attack upon its very soul." And by the end of the movie, some of the Son'a are on the planet. Picard said he would visit. I doubt the planet stays as obscure as it is in the beginning of the movie, but that is never talked about in the movie.
This is a moral like any other. If Picard was asked to murder 600 people, would we be screaming that it wasn't enough of a moral dilemma? This is the 24th century where the Prime Directive is as much a part of law and morality as the laws against murder are today. People tend to overlook that when asking these questions.
And to apply it to our world, how would we treat the Middle East differently if we never had oil interests? What else is the Federation willing to do from this point forward for "medical advancement?" As Geordi says, "How can I look at another sunrise knowing what my sight cost these people?" If we didn't have to play footsie with people for their resources, would we keep our moral high-ground? If the movie depicted the way women are treated by Saudi Arabia, for instance, would we still think it's a clunker?
I think there's a lot of merit to this story. I think the "fountain of youth" is overplayed. This is about ending disease and genetic problems that remain unsolved in the 24th century. The problem with peace is that it leaves you defenseless, as the Bak'u are not willing to defend themselves. And this is about the moral equivalency to killing off 600 people for scientific research, say a cure for cancer or AIDS. We have laws against those kind of experiments now. But we have a study where babies are never touched. If we can see that as progress, why can't we understand we are judging 24th century by 21st century morals?
The ONLY criticisms I have of the movie are the lighthearted comedy and the fact the Bak'u are all white and thin.
Also, the only way to keep the "fountain of youth" if the Bak'u leave the planet is to take injections--technology--for the rest of their lives. That's destroying who they are. So it's us or them.