3.>With the Ba'ku the orders were based on a false assumption. Once it became known that the Sona and Ba'ku where the same race. the Prime Directive kicked in. i.e Starfleet officers should take all steps to avoid becoming invovled in the internal affairs of other races.
What "false assumption? Anyone on the surface of the planet would be killed when the Federation and the Sona harvested the particles in the rings. Whether the Baku and Sona have (or don't have) "internal affairs" doesn't change that fact. The Baku had to leave. Yes, the Federation should have initially asked them to go under their own power, but they did have to go.
Hard to see how the Prime Directive would "kick in." Once it is realized that the Baku are both refuges and a warp capable culture, the Prime Directive is irrelavant. And once the Baku and the Sona are seen as one people, that just means that the Baku have somewhere to relocate to (a Sona planet), off of the Federation planet that they reside upon.
Or do you in general force people to do your bidding when you think you know what's best for them?
If the Baku remained on the surface, the harvesting of the particles would have killed them. If a police officer encounters a person in a building about to be demolished, if a firefighter encounters a person in a building that is burning, they don't ask that persons permission before removing them.
Relocating the Baku was for their safety.
And if the Federation Council, after their review, didn't continue the process of harvesting the rings particle (after finally removing the Baku), how many of them would end up in prison?
Certainly after the general public found out that the Council deigned the Federation of the health advantages of the particles, just so that a small number of pretty people could live undisturbed in a single small valley, the majority of the Council would be remove from positions of power.
You know that "never ask when you can take" is a Ferengi and not a Federation rule, do you?
What do you mean "take?" It was a Federation planet and they were Federation particles. Who were they supposed to have asked?
If the S'ona simply wanted to exterminate the Ba'ku ...
The thing is, they didn't. The Sona went out of their way through the majority of the story to prevent harming the Baku.