First, the baku are more like trespassers than legitimate owners. And trespassers are evicted.
Second, if the baku somehow own the land their village is on as per federation law (600 in a small village owning the entire planet is absurd), as I already said:
"Indeed, the clandestine plot was idiotic.
The federation council should have invoked eminent domain through the legal channels. Assuming the baku had any legal right to the planet under federation law, that is (it doesn't look like it)."
Invoking eminent domain implies, of course, just compensation (and proving public interest - easy to prove, in this case) AKA giving the baku other land to live their preferred lifestyle and giving them priority to the medical advances that will ensure their continued immortality.
And if the baku would refuse this because they can't be bothered to use hyposprays, these being not pastoral enough for them - frankly, giving into such demands of egoist assholes at the cost of all the suffering the medical advances could prevent is immoral.