On the topic of unwanted civilian ships, I'm very protective of my TNE supplies, and I don't appreciate having the private sector raid Staurn's Strategic Sorium Supply with their undersized sorium harvesters. Whenever one is built I tractor it with one of my tugs, which confiscates the ship and gives me control over it. Then I scrap it, and if I'm feeling generous I subsidize the shipping line.
In principle this should work just as well for your colony ships, though it's easier to target sorium harvesters because they show up as a target for refueling purposes in the task group window. I've never tried to confiscate colony ships. I believe it was sometimes done in the days before shipping lines retired their old ships, for the sake of speeding up the game.
EDIT: Deleted second suggestion that wouldn't work.