Civilian ships does appear in the "manual tractor" list of any tractor-fitted ship in the same location (you can find this popup menu list in the ship information window, the "miscelaneous" tab which also allows manual fuel and supply transfers).
As Colony ships and freighter usually takes a few days to load or unload, you've got a window of opportunity to just seize them and destroy them in whatever way it pleases you.

And for preserving the strategic sorium reserves, just ban the body (System information window).

If the phantom ship is still on its shipping line's fleet list you might be able to select it and use the Clear Orders button. Or perhaps this would only work preemptively, clearing the orders just before you tractor the ship. How did you delete ship? I always abandoned it and set my salvagers to work on the wreck, and I never encountered this error.

Nice and automated, me like that. And the rpl btn grows back its strength by being on a friendly planet without hostile?

As for the trick of tractoring a civ ship to acquires it, it works, much praise and karma to you Prince of Space 

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.