As for the "kicking their ass in self-defense"-how does that apply to the movie? The Baku didn't win the fight, they had someone else do their fighting for them. If your point is "have the Baku fight it out with the Son'a," then I'm fine with that, but the Son'a still win. It doesn't exactly endear the Baku to the audience that they are "pacifists" who are happy to let others risk their lives and fight on their behalf. And the ending pretty much guarantees that the UFP will be committed to defending the Baku from now on. I'm sure Starfleet officers are thrilled about that prospect.
Defend them from what the Son'a and the Baku want to try to getting along again at the end of the film.