Well, it could be made like, have two clans agree on war over a certain country.
In that country an arena forms, where one player logs out, and he "claims" that arena. Opponents from the other clan can attack him, and if they win, the original player is removed from the arena and can no longer participate in the war.
The module keeps track of how many wins each clan has, and, when the certain number is reached, that clan wins and gains surpremacy over the country. They can have a bonus, maybe 10% lower costs in the shops or 10% cheaper healing. The losing clan can have a random rare event where they are stopped by guards in the village and have to fight in order to survive.
And if a certain number of game days has passed with no clan achieving victory, then it is declared a draw and no one gains any benefits/losses.
Plus, one clan can only hold surpremacy over one country.
The way I see it, is that it would first encourage some kind of planning and coordination between clan members. It wouldn't do any good to put your strongest member first, but if you put weakest member you would just give a free win to opponent. The tactics that would work best is to have someone just strong enough to defeat a present enemy and keep your strongest members back, so that they can enter into the game later and kick others to secure victory.
Secondly, it would discourage clans with only strong members. If some clan with only top members gets in a war and has one of its members "claim" the arena, the other clan, that has no members who can oppose him, would just ignore him and the battle would end in a draw.
Thirdly, it would discourage genin/academy student clans, since they would not have members strong enough to do anything.
*shrugs*
That's just a concept. Surely someone could expand on it or come up with something better.