The Council didn't know that Baku were warp-capable. In fact, they were led to believe the Baku were a primitive, pre-warp culture--hence the duckblind mission and worries about the Prime Directive. Once it turned out they were not
pre-warp, the PD didn't apply. This was specifically mentioned in the movie.
That the Federation was willing to surreptitiously move a pre-warp culture to another planet is pretty unseemly in itself, though. They weren't willing to move such a culture in order to save them from certain destruction ("Homeward"), but they were
willing to forcibly move a pre-warp population to get at a natural resource, Prime Directive be damned. I guess forcibly relocating a planet's population doesn't count as "interference" to Federation bureaucrats.