As far as I know there are no indigenous civilizations in the star trek universe who look at the federation and think “nah I’m good, leave us alone please”.
There’s an episode in The Next Generation, I think called First Contact, in which a civilization on the verge of FTL travel is covertly contacted for Federation membership but they ultimately decline. The reason they decline though is because a lot of their population is very reactionary and their worldview would’ve been completely shattered by knowledge that they weren’t the most advanced and important species in the universe, and the head of state decides that such a thing would cause far too much social upheval and declines the invitation.
There’s an episode in The Next Generation, I think called First Contact, in which a civilization on the verge of FTL travel is covertly contacted for Federation membership but they ultimately decline. The reason they decline though is because a lot of their population is very reactionary and their worldview would’ve been completely shattered by knowledge that they weren’t the most advanced and important species in the universe, and the head of state decides that such a thing would cause far too much social upheval and declines the invitation.