Where as Dougherty was going to bring a incredible medical treatment to hundreds of billions of people, simultaneously inconveniencing a few hundred people in one little valley, on a Federation planet (a fact the Baku never refuted).
Would you move six hundred people for a cure for cancer?
Would you move six hundred people for a cure for AiDS?
Doughtery was willing to make that "faustian bargain," plus he was acting under orders from his government.
You make a good point about the ends seeming to justify the means, T'Girl.
However, in this case the Ba'ku were being covertly monitored by the Federation. They were misled to believe the Ba'ku are a primitive species, so they hadn't yet made contact. After the failure of the Duckblind mission exposed the Federation to the Ba'ku, it would have become an opportune time for Dougherty to begin some diplomatic discussions about the benefits of the Ba'ku planet and to allow the Federation to perform research there. Of course, it would be a difficult diplomatic task, as the Ba'ku are averse to technology.
The health of the Son'a leader Ru'afo appears to be deteriorating. He desperately wants to extract the beneficial radiation from the Ba'ku and pressures Dougherty accordingly. But the big mistake in all this is that all Ru'afo would need to do is hide out on the planet surface for a while--he'd be healed! But he and the Son'a are angry at the Ba'ku for banishing them many years ago and want to take over their world. And, the process of extracting the beneficial radiation would destroy the planet. Rather misguided, killing the goose that lays the golden egg so that you can get a bunch of eggs up front, rather than being patient and taking an egg each day.
The corruption resides with the Starfleet officers who have conspired with the Son'a to take over the Ba'ku planet, namely Dougherty and his contacts in the Federation. Dougherty would be a co-conspirator on the Son'a intention to destroy the planet. It is true that he was seeking to gain the healing benefits for the Federation, but doing it in a very unethical manner. So... he's not an "evil villain" per se... but an unethical man all the same.