Why not just have settings similar to other aspects of the game? Allow us to set a cap on the number of civilian companies and/or ships (or history length or whatever other pertinent parameter there is). That gives a little more flexibility that the either/or choice we now have.
If an automatic 'just right' solution exists then there is no need for manual fine tuning. Limiting production of classes that already have idlers has the benefits of being relatively simple, scalable, and fully automatic.
I'd love both a limit on the number of ships AND ability to influence what they build. So if they want a freighter I get a window where I can say Yes you can build it or No you cannot. Might be too much work, but I could tailor the civilians to do what is most needed instead of doing their own thing.
That would be giving the player too much control, and the popup spam would quickly become intolerable. Civvies are supposed to act independently, for good
and ill.