If we have a war, let's just do it the old fashioned way: no fighting in the villages until a certain point is reached.
For example, war starts between Konoha and Suna (I think we know who would win IF that forbidden event were to occur) Konoha can't just go ramming into Suna like a bulldozer. It needs to "secure" areas in the zone first, particularly the desert zone. I mean, why not have some of your defenders in the zone areas we like to travel in a time of war?
Then, after that's "taken" or whatever, then Konoha can start moving in to attack Sunagakure, the actual fighting happening in the Empty Town Zone if they would rather not have their board taken up. They just need to remind people that the village itself is technically having issues with invaders if so.
Now then, addressing the council, I forget how many GM's there are, but I agree with that notion. If they screw it up, not many other choices on who can do it better.
If push does come to shove, you could just start the fight in the village board, then transfer it to the Empty Town Zone. Now, I understand that's then taking up a zone (unless someone wants to constantly pay for a private zone. Like, funding the field of battle of sorts!) but at least the village board is... somewhat free. People still need to act like their village is under attack or something...
Lastly (for this post
), regarding the schedules, we need to schedule almost the entire war:
Day 1: Mobilize. Zone travelling areas open for combat.
Day 2 (doesn't need to be next day): Results from Day 1 taken into account
Day 3: Results from Day 2 taken into account
And so on and so forth, till you get to the maximum number of days that you "have" for this war, determined by a combination of the attackers and the GM's:
Day 100 (I doubt many will be fighting for this long buuut...): War is concluded, with all overall results taken into account to determine winner. Once determined... Winner gets something I guess.
It's a rough picture, I know, but ideas too.
But, since it's so rampant, it apparently isn't. 
Anyways, with half the population choosing Rinnegan, peoples like me are going to have to start god-modding a bit more in order to start getting zone kill counts... Then the rain will start dropping. 