So the Federation council just decided that Starfleet should ignore General Order Number One (aka the Prime Directive) you know the one that says don't interfer with other species.
If you look at the history of the Federation and Starfleet, this isn't that unusual. Other planets that would have been consider to have been under the prime directive have been "interacted with" before.
Eminiar (stipulated to be non-warp) was contact to establish a "treaty port." Treaty ports are areas that are open to foreign trade, are legally extra-territorial, and are removing from the control of the local government.
Janus Six, a mining facility was established to mine natural resources
, no consideration was give to whether there was intelligent life there. When intelligent life was found, it was put to work digging for ore. No dialog as to the planet belonging to the indigenous Horta species, or the Humans leaving.
Kirk: " She and her children can do all the tunneling they want. Our people will remove the minerals, and each side will leave the other alone."
The Halkans were contacted by the Federation to so that the Federation could mine a natural resource
(dilithium), the Halkans were not indicated to be a post-warp species.
Capella, the native people of that world were contacted by the Federation so that the Federation could mine a natural resource
(topaline), the Capellan were obviously pre-warp.
The argument could be made that the prime directive by law
doesn't apply when needed natural resources
Guess what moving them is interferring.
Moving them is what was going to keep the Baku from being killed by the harvesting process. If the particles could have been gathered without the process killing them, the Baku could have been left where they were in ignorance.