Hm, I imagine the fix here would be easy to implement: Any war in which one faction has achieved 100% war score (total victory) should automatically end as soon as the defeated party capitulates. There are reasons to refuse an offer of capitulation if you're still fighting the war, such as weakening them further for your allies, but once it's over it's over. There's no reason the victor should have to agree at that point, as the only reason he wouldn't would be to game the system.
There'd still be the potential for exploitation, but at least at 99% war score the opposing side still gets soldiers from some holding, somewhere, however small, and could potentially get enough for a siege.