So the Feds didn't learn their lesson from the Organians? Just because a civilization looks like it's undeveloped, and you think they won't notice being moved during the night, it doesn't mean that they don't secretly have the power to bite your arrogant ass off and spit it back in your face. If they wanted to.
Guess what? The baku don't have the power to enforce any of their claims.
And if you think the federation arrogant, you haven't been paying attention to klingons, romulans, etc - or the good old USA, China, etc.
Why not make first contact and explain the situation? They might just volunteer to move, for the "needs of the many." You're screwing with them anyway, why would you care if they suddenly became aware of space travel?
What you just described is eminent domain. Its first stage, that is.