The bottom line is, the Ba'ku would not have noticed anything was amiss until after they'd been quietly abducted--most likely while asleep. That gives the Son'a a lead time of at least a few hours to start up their collector and make the planet uninhabitable for the Ba'ku. Since the holoship was a Starfleet ship under Starfleet control, Ru'afo was not going to be able to destroy it--unless his plan was to screw over the Federation, too, by killing Dougherty, destroying the holoship, and making off with the magic particles himself. In that case, why even bother with the subterfuge? The Federation would hunt him down and destroy his fleet anyway.
If we can assume Ru'afo isn't a complete idiot, his plan seems to have been the following:
1. Cozy up to the Federation so he can get access to the Briar Patch without a fight.
2. Convince them to relocate the Ba'ku so the particles can be collected.
3. Once the Ba'ku are on the holoship, release the collector, get the particles, render the planet incapable of supporting life.
4. The Ba'ku realize what's been done, but it's now too late to stop it.
5. The Ba'ku convince the Federation that they aren't actually backwater bumpkins, but a technological civilization. By this time, the Son'a have already gotten their particles and likely high-tailed it back to their own empire, leaving the Federation with some magic particles and
This plan makes the Son'a look pretty scummy, but perhaps not bad enough to provoke a war with the Federation, especially since the Federation risks substantial embarrassment at having been duped. They'd probably want to keep the whole thing as quiet as possible.
It's quite a cunning plan if you think about it, and it doesn't require Ru'afo to fire a single shot to get his revenge.