OK, they could do it (though if you're ignoring one of the fundamental properties of the omega molecule, why not just ignore all the problematic properties of the omega molecule?). So the Federation has scorched an entire volume of space (permanently) to stop a fleet from traversing it temporarily. The problem - the war - is not solved, it's just slowed down. I imagine the Dominion would just send ships through the disruption at slower-than-light speeds. They've demonstrated that they are a patient civilization. They wouldn't call off a war just because the trip to the fighting would be too slow!
Alternatively, the enemy fleet either goes around the area, in which case you've just bought some time by creating a permanent disruption in traffic, and given them
a reason to do the same to your
side. Send a changeling to Earth and have them detonate an omega molecule at the heart of the Federation. You've escalated the war.
Or the enemy just finds another way through the disruption. For instance, would a slipstream drive be stopped by an omega molecule's disruption? Or would a transwarp tunnel be affected?
Anyway, it's an over-reaction. It's boiling away the oceans to keep the enemy navy from reaching your shores, and destroying the atmosphere to keep the enemy bombers from flying over your cities. Why do it?