The Ba'ku can be immoral if they like, you and I may not like it but such is life. The Ba'ku wer initially thought to be pre-warp as such the Prime Directive applies, once the connection between the Son'a and the Ba'ku was discovered it became an internal matter between them also a Prime Directive matter. So to up hold their ideals the Federation had no buinsess being there in the first place. Sometimes upholding your ideals/morals puts you in a weaker position.
Really given the planets location within the Briar Patch the Son'a might have been able to go and do the deed without the Federation being aware of it.
But as you say the clandestine plot was absurd.