If my alliance Destroys our own AC4, Will we lose points in DD?

In the Doomsday wars the points will be better the more Alliance centers you have. So if you only have 3 or 4 you will gain less points during the war. You can still sin if you destroy the other alliances centers or you can still earn more points than them so it may not stop you from winning but it will make it harder to do so.