Non sequitur? Not at all. It's very germane to whether the Baku are the ones who control the disposition of the particles.
600 people preventing billions of people from receiving an important medical advance, a medical advance in orbit around a Federation planet, why would the Council be "tolerant" of that? Why would the many people of the Federation be tolerant of that?
If the Baku are taken to a different Federation planet, they can have the same access to the collected particles as the rest of the population, no less, and certainly no more.
It's important to keep remembering that the Federation doesn't want the Baku off the planet, so the Federation can use the planet themselves. The Federation doesn't want the planet at all. They want the Baku off, so the Baku won't be harmed when the particles are harvested.
In generations, when the planet recovers, the Baku could conceivable re-establish their community. Assuming they would wish too.