Freelancer is full of these little scientific impasses that you need to gloss over to keep the illusion going.
The fact that ships have the endurance to withstand repeated bombardment from particle blasters and sun coronas but can't handle the stress from re-entry is but one of them.
To me, docking rings are in place to allow ships that can't handle said re-entry access to the planet. They also make getting off-planet easier as there is no massive energy burn needed to attain exit velocity.
The fact that they also provide a means of controlling access is just the icing on the cake for Ageira, and those that control said planets.