I would love player controlled trade nodes. It could be established with a structure similar to the admin command and handled by Sectors (so we could incentivate creation of more of them) and you could drag in ships directly from the civilian list.
Eventually a new Trade Node screen similar to the Sector one could be created of you dont want to link it to sectors
You probably could find this as rather useful for player logistical use as well to reduce micromanagement. The system could be expanded to incorporate both mineral, trade goods, infrastructure and planet buildings all in one system.
If a player want to disable the civilian traffic the player could themselves build all the "civilian ships" and just assign them to these trade routes and the system will automatically load and unload based on demands.
The player could mainly be in control of building up the trade node network much like sectors with trade station levels and assign the relationship between them. The AI probably could cheat a bit and upgrade/downgrade based on the most convenient trade network needs over time.
If I make a demand on a planet that demand will be placed on the local node and then up the hierarchy and the system would make sure that the right stuff is eventually delivered to the location in question by the local distribution network. Obviously some system don't have a local trade node so some trade nodes will still service other systems close by.
But I could see such a system as an improvement to the game in more ways that just civilian traffic but for all transportation of goods from minerals to supplies and even ammunition. The player only need to make sure the system is greased by the right amount of ships and make sure to build of the infrastructure to create the nodes and then it can simply live of its supply and demand.
A player can still make separate transportation routes but I think such should be more expensive in terms of wealth to create rather than use the trade network who should be much more efficient, but sometimes economic efficiency is not as important as strategic efficiency. This way you could introduce a wealth cost for manual transportation of goods no matter what it is but using the trade network is more or less free except for the fuel.
I think all ships should pay fuel costs, even civilian ships should cost fuel. If there are no fuel available to the civilian fleet it will halt moving, that would also mean that civilian fuel harvesters do something and not just deliver some wealth.