Hey, i was thinking about the bases in the map. And i think they should be bigger, just a little so there can be some Units guarding them. You can give those units to players but make them unable to leave the base.
Like in Konoha, there could be some ANBU guarding around, and the heroes (players) should be able to buy more of them (Some gold and 1 food with a cap of 5 for example).
Also make that only the matching players of the base can hire units, that way it will be fair (Train units instead of hire them like a tavern).
And when another player owns the base, just kill every "Hired" unit and set the players of Konohas food cap to 0. Im sure it can be done...