Ehm, you know the Prime Directive, do you? It is not the job of the Federation to judge or even interfere into the internal matters of another culture. The Ba'ku could slaughter the Son'a or vice versa, it is none of our business.
Furthermore the Ba'ku exiled a bunch of people who wanted to explore the stars anyway. No idea how a bunch of peasants are supposed to be able to force the younger generation which has warp-capable spaceships off the planet. The older folks could not even have thrown the younger folks out of their villages if the latter had particle weapons. So it wasn't a matter of force but had more in common with parents telling their children to get lost. No physical harm done but the relationship is damaged.