Following the analogy that this is WAR, a couple of suggestions:
-Saboteurs and fifth columns are a known threat in any war. In reality they are shot. I propose that we allow anyone to switch a tag on another player that changes them from green status to yellow. Then they can be killed. The attacker would also change status to allow other players to take down an assassin. Have your NPC’s aggro on yellow players with the ability to immobilize them. This opens up other mechanics that might be interesting. Have a bad commander? Tag him yellow and frag him. Players running from battle? Have your Rangers shoot em down.
-Allow players to drop off supply in dumps as well as pick up. This would allow some mitigation of the saboteur’s effect.
-Allow the destruction of unwanted seige. Again this helps to mitigate some of the damage. I would also add an area wide alarm if seige is being damaged so you can mobilize and prevent the unwanted destruction of seige.