There's a number of hard/soft locks to prevent most blatant exploits:
- Siege can only be started with a military capital ship with high enough class - so attackers must have always at least one capital ship they are willing to sacrifice
- Siege established a relatively large (say, 200 km diameter to start with, but can be also a lot larger if needed) warzone, which locks civilian capital ships from entering it and ones staying inside unusable
- Civilian capital ship shield only allows a relatively low number of passing ships per certain time - meaning that it can carry a fleet but fleet can't enter or leave the ship at once. If you get only one ship out per five minutes the opposing side has easy task with destroying them one by one. Similarly the fighters can't escape to the safety of the civilian capital ship, as only a few would get there.
- If the fight takes place inside the belt civilian capitals are either locked out or have to park at the docks, which means they will be locked out once siege starts
As Civ Cap Ship are invulnerable it to me seems just better to not risk anything and keep "sieging them" by camping them.