Exactly. Under ideal conditions (and yes, the conditions in INS were not ideal), if Our Heroes primary concern was the Prime Directive (and that's a big if under the circumstances) they would have stood (standed?) down and withdrawn from the planet as soon as they became aware of the relationship between the Son'a and the Baku, for the same reasons they withdrew from Klingon space in "Redemption".
Well you said it yourself that conditions in INS were not ideal so what would you have the characters do let the Son'a kill them?
Well, the Federation pretty much let the Cardassians kill much of Bajoran population.
Seems only Federation members are entitled to protection.
If the Son'a had been smart they would have transported the the Baku off the planet themselves and not gotten the Federation involved. We aren't talking about billions of people here, only 600.