On one, I don't think that a part of the PD, but rather a admissions rule instead. A planet probably could still have factions, political parties, opposing viewpoints, what have you, as long as the majority of the planet isn't being torn by civil war. The Bajorians certainly didn't alway get along with each other.
On two, there has to be a practical side of the things in the real world/universe. If the Federation needs a resource, and a unpleasnt group is the best provider of tha resource, well it's their world, isn't it?