The civil war ended when Alliance heroes defeated VanCleef and destroyed the last remnants of the Defias. The Alliance triumphed in Westfall as the Defias are no more.
As for Duskwood, since all those who went rogue were vanquished, we can reasonably assume that the town was retaken by the Alliance. The town itself was never destroyed, only some of the Night's Watch turned to the Legion, but they were all slain by the Rogue player.