It won't auto end until the guild leader/vice guild leader choose to end it. It gives others a chance to rack up personal contribution to get all their milestones. Some of my guildies kpkb when the guild finish all domination too fast and they don't have the chance to get 5k.
So our guild leader made a point to have some allowance, like half a day to one day for all who are interested to get 5k, before starting a new guild war.
My guild runs 2 wars per week, Hard and Nightmare.
My guild leader will start the first war on Monday on Hard. But my guild has super On members that complete full domination in one day. My leader will only end the war by the end of Tuesday.
2nd war at Nightmare starts on Wednesday. Today is Thursday only and 4 towers are dominated. Even if we can finish the domination by today or tomorrow, my leader will only end it on Saturday.
In the mean time, everyone gets the chance to sweep the easier 100% dominated towers for personal milestone rewards. Since every week there can only be 2 wars, ending early does not make any difference, and its more considerate to members who cannot play at certain timing, giving them the chance to get milestone rewards.