The Founders weren't of quite the same stripe as other races the Federation had warred with. When they fought the Klingons, it was Klingons who died in battles. Same with the Romulans and everyone else. But it wasn't Founders who died in battles with Federation, it was Jem'Hadar and the odd Vorta - beings the Founders designed for just that purpose. It's a different dynamic, one where the ultimate opponent has far fewer incentives to seek peace.
The question isn't really about whether or not the Federation was worth saving. The question is whether the Founders were worth preserving. It's not as though there were dissident Founders who never wanted war with the Federation (Odo doesn't count). There were no civilians or innocent bystanders. Section 31 succeeded in changing that asymmetric dynamic.
The Founders' entire reason for their outlook was the belief that 'the solids' were a threat to their existence. By reasoning from that axiom, they managed to make it true.