Sure, they obviously needed the Federation. Doesn't mean that they might not have manipulated the data to exaggerate the medical benefits of this funky radiation, doesn't mean that they wouldn't have stabbed the UFP in the back if Picard had not interfered, doesn't mean that Dougherty's "let's trade-off lives" calculation is not totally obscene and wicked.
They didn't need the Federation to simply exterminate the Ba'ku. You don't think that Federation scientists looked at situation and ran their own experiments to back up the S'ona conclusions?
It never ceases to amaze me how people look at the move of the Ba'ku in a vacuum, to paraphrase Spock: "even morality must give way to reality".