Well since it's siege, it shouldn't be worth for a siege starship to hit turrets either, perhaps other economic buildings?
That being said, how about splitting siege starships to : 1 with large bonus against large buildings such as command stations and force fields but cannot attack fleet ships or turrets, the other 1 with large bonus against turrets only and cannot damage/low damage against fleet ships and large buildings
As for large bonus against fleet ships or starships, that's the job of the rest of the army
( but you can consider adding the starships to the "large building" list)