Consumer goods and survival resource shortages have three effects: TL regression, deaths, and social order penalties. I believe that it is the social order penalties that eventually incite civil war.
The TL-regression-due-to-shortages mechanic actually helps the planet get out of a resource shortage state by reducing consumer goods demand. A foundation trade route will continually pull a regressed planet back into a higher demand state, which aggravates shortages. These repeated shortages, which would not occur without the external pull from the foundation, will cause the planet to go independent abnormally fast.
IMO this is undesirable game behavior in a game where players are likely to be inactive for multi-hour stretches. It should not be possible for a planet in civil war to gain TL through a tech project or foundation link until the civil war ends.
Fixed in Era 4.4. Tech level does not increase if the world is in revolution or under siege.