No, it wasn't supposed to destroy the biosphere or the ecosystem. It was supposed to kill humans, while leaving the planet habitable for other humanoid species, explicitly including Cardassians.
I used to think that evacuation would have been flat out impossible, too. But Sisko gives the locals fair warning of what he's going to do, supposedly "less than an hour" in advance. And lack of ships need not be any sort of a problem: these people arrived here on ships, fairly recently at that (in the aftermath of the old war with Cardassia, supposedly, and that one was still going on in the early 2360s) and we never were told that they would have merely hired the transportation.
As for the population of Solosos III, it certainly didn't number in millions or even hundreds of thousands. After all, Eddington says that only Sisko's intent to escalate his campaign to cover all Maquis worlds would make "hundreds of thousands" homeless. That gives an average population of mere thousands for the supposedly hundreds of worlds in the disputed areas, and jibes well with what we saw of DMZ worlds before this.