I have 2 solutions to this problem. First give the sieges an anti personnel weapon. Similar to the ones in IOC. This would be key since by the battles very nature the defenders are left outnumbered somewhere and having the siege could make the difference. Second if the attackers destroy all 3 towers it should end the battle or force the defenders to have to control all 3 bases,
The solutions would not only makes sieges somewhat useful, but it would fix the problem of defenders having an advantage.