Introduction
Here I will be describing a possible fix and new addition to the game that will allow for Spacestation-like properties to exist on ships without having any freedom-restricting features in the game.
I will be detailing changing some existing blocks, and optionally adding some new ones.
Change factory block weight, power consumption and some behaviours.
Easy solution: Increase the mass of factory related blocks.
This solution is a straightforward and easy solution to this whole dilemma; only the largest of ships would be able to field factories. Not only would it not affect currently existing planets and spacestations, but it would very adequetely balance everything out- the only factory bearing ships would be large and slow, with lots of power alocated to factories(and less to weapons).
Unfortunately, there are many problems with this, and it can only be added AFTER combat editting is completely done for, so that people don't delete factories quickly while going into combat. In other words, this would need to be added after the shipyard update(should it be added.)
In addition, the block weight would need to quite high- while I don't know any exact numbers for balancing it out, my best guess is 100-255 mass per block.
Behaviour change(added with the easy solution to form the slightly less easy solution): Make factories consume a little bit more power and have a "charge up(and power off)" time.
This solution is less obvious, but it will naturally limit ships that want to be super powerful destroyers while still having factories. It will not dis-allow them, but it will still naturally limit them, making it more difficult.
Basically, the "charge up(and power off)" time will make it impossible for a ship to just immediately turn off the factories and be combat ready. When a factory is turned on or off, it takes a few minutes to fully switch on or off, and during that time, it consumes power as if it were running. This means that ambushes are a bit more valuable, and factory running can be a bit more cautious.
This would also mean that capital ships would have to be defended by frigates or smaller ships while they're powering off factories. Note: None of the defense from frigates is required, and any ship, should they want to, can simply add more reactors and be able to have enough power to support weapons and factories at the same time.
Now, for the increased power consumption, this will also naturally bring ships closer(or farther beyond) the power reduction curve, making them larger and less efficient for movement. It's a step closer in the right direction for cap-ships without some restrictive or unrealistic features.
Second option: Greatly increase power consumption of factories and add a new line of "industrial" blocks.
To be honest, this solution was tacked on at the last minute and I haven't thought about it at all really, so don't take it seriously.
Basically, the power consumption and mass of factories would be increased by a lot, and then a new bit of things like Industrial Reactors would be added, and these would be far more expensive, weigh a LOT more, and also produce quite a bit more power.
That way, space-stations can remain relatively unnaffected, while ships that want to be able to produce with factories would have to use heavier blocks that cost more(And from getting those heavier and more expensive blocks, it would balance out the lack of purchase of a space-station).