I propose that when the winning team has all 7 flags, the base defenders should no longer use the "Base Defense" skill, and the players should be able to enter the zone and kill an NPC that would be guarding the altar (which would also have the Base Defense skill anyways, preventing spawn camping and teleporting assassins). This NPC (possibly called Luxon or Kurzick commander) would be a different class than the other players, so it wouldn't be affected by EOE, and would have lots of health. Once this NPC dies, the attacking team should win and get 1000 faction for a 'decisive' victory. If for some reason the defending team captures a flag, all the base defenders and this NPC would regain their "Base Defense" skill and would nuke everyone within the base.
What does everyone think?