Let’s put politics out in the open and turn Alliances into Clans and make Alliances a group of Clans. When we get to the War Map, we know who is already allied.
Then you can have wars chosen by the players. An Alliance will declare War on their enemy and the War will start in a chosen time. The Clans fill up the War Map and duke it out. The torch system will be the same. Wars can be 2v2, 3v1, 2v1, and 1v1 pending on clans joining. If each side has two clans joining then it will be 2v2. If you have beef with 2 Alliances at the same time then the remainder clans will have to fight. If there are no clans to fight at the time, they will have to wait until the end of the battle. But the next fight goes to the Alliance waiting. Unless you are merciful and want to add a rest period of 24 hours. The Alliances know who they want to fight let the players choose their enemies instead of sticking unknown allies on war maps.