Starfleet can't "break" the prime directive with the Kelpians (bring Saru back, start relationships, give them technology...).
But Starfleet
can absolutely and
should "free" from other outside interference. In TNG "Redemption", Starfleet
absolutely could interfere in the "internal" Klingon Civil War as soon as it became apparent they weren't really internal affairs, but powered by outside interference from the Romulans. In TOS "A private little war" it was absolutely allowed to "restore" the power balance on the planet after Klingons gave one fraction advanced weapons. In ENT "civilisation" it was
absolutely right to chase away the aliens that made experiments on the pre-warp planet.
The prime directive stops everyone from interfering in their
internal affairs. Once another outside force
already interferes with someone - it's not "internal" anymore. It's the absolute right and lawful thing to try to stop and reverse that interference so that the civilisation can go back to it's own, natural way.
The only reasons why they don't stop the Ba'Ul might be either
- Realpolitik (maybe a peace treaty that grants them Kelp, in return for peace and them not harvesting any other planets), or
- the Ba'Ul and Kelpians being the same species/from the same planet (thus it being an "internal" lifestyle again).