Is there a way to get rid of unused fortresses within the alluane territory?

When a fortress is destroyed in your alliance territory, all buildings within its borders (usually alliance resource supply depots) will also be destroyed. Otherwise, if what you wanted was to simply transfer your hive to a better resource location, simply spawn a new fortress to the new position and the unused ones will automatically be removed -- if not, will be suggested automatically. Take note though that only alliance leaders can perform such things.

If your alliance keep hitting that fortress eventually it will automatically teleport away