Well the episode states that a detonation of an unstable molecule makes a large area of space unable to sustain a stable warp field. So ceding your point of the Federation being able to create one, use in the manner you describe could bring the war to a stalemate. Though this really seems something like Section 31 would do.
Well if the Federation's going to break out superweapons, why not dust off the plans for the Genesis device? So what if it's not stable, that's still a hell of a weapon. Wipe out entire enemy planets and I'm sure detonating one among their fleets won't be healthy either.