MacLeod, as per the movie Dougherty told Picard from the beginning that the prime directive doesn't apply because the baku (and then, the sona) are not natives and interfering doesn't disturb their natural evolution.
It's been a while since I've seen the film, but I thought it was only after Data went crazy and Picard spoke to Sojef that he found out they were not natives. Picard is the one who tells Dougherty that the Prime Directive is unbroken in his report. I'd have to rewatch to be sure though.
If Starfleet knows from the start the Baku are space-farers, why bother with the duck blind?