Except, up until the end of Insurrection Ruafo and the rest of the Sona were going out of their way NOT to kill the Baku.
But probably only for show. They needed Starfleet to believe in the goodness of their plan, after all.
Had they really been able to move the Ba'ku to another location, though, the Ba'ku would immediately have raised holy hell, as they were not
primitives incapable of realizing what happened. So it would definitely be in the Son'a interests for the holoship to have a little "accident" of one sort or another...
Rua'fo really hated the Ba'ku for their good looks and the disgusting habit of spewing apostrophes everywhere. Making them suffer must have been a major part of his plot from the get-go, and he could spin any sort of technobabble at the ignorant Feds to justify his destructive approach to personal rejuvenation so that this suffering would be ensured. Ultimately, elimination of witnesses would be necessary, though - after all, if the Son'a didn't have to fear retaliation from the Federation's part, why would they need to beg for UFP permission to mess with the Ba'ku in the first place?