Surely just being in Federation territory doesn't make every planet in it under the control of the Federation. The Federation is not a military dictatorship, is it?
And surely after 300 years the Baku and Sona have some rights to their planet which should be recognised no matter how inconvenient?
I see to remember some episodes in TOS where the Federation wanted some dilithium or herbal medicines or strategic value from some planets but accepted it when they said No. Have things changed by the 24th century?