The Sona and Ba'ku where members of the same race, and the Sona disliked the fact that they had been kicked out. It seemed as if certain information which might have altered the Federation/Starfleets decison was withheld. So whilst they debated the resettlement of the Ba'Ku they did so without all the information.
Had they known the full extend of the relationship between the Sona and Ba'ku it is possible that it would appear to violate General Order 1 they might have said no.
Non-interference is non-interference.
Which would've meant they would need to stand back and allow the S'ona and Ba'ku to fight it out. Which would've led to the extermination of the Ba'ku.
Non-interference is a bitch.
Starfleet and the Federation really were doing the most practical thing possible in this situation. They couldn't afford to fight another conflict while in the midst of the Dominion War. They more than likely couldn't afford the resources to protect the Ba'ku from the S'ona, which would violate the Prime Directive. Then there's no telling who the S'ona would've teamed with to obtain the particles if the Federation had said no.
So the Federation really had three simple choices:
Move the Ba'ku.
Protect the Ba'ku.
Or essentially declare open season on the Ba'ku.
Yes they'll return to their normal lifespans but they won't die bloody, pointless deaths. YMMV.