Have you tried doing some 5 second increments?
If that doesn't work, there's a trick where you can coopt civie freighters into your fleet (where you can delete them) by using a tug - you should be able to search the forum for it. To get the tug, design one, go into SM mode, then create one in Fast OOB mode. You can then put a waypoint at the location of the civie you want to get rid of and change the location of the TG containing the tug by using SM mode.
John
PS - btw, the designer password wouldn't help, since civies are not another race. Editting the DB is a bad idea too - in addition to removing the ship from the DB you would need to remove all records (e.g. the civie TG) that refer to it. If you messed up, you'd end up with a corrupt DB. This is why Steve is conservative in giving out the DB PW - he doesn't was spurious bug reports from people who've messed up their DB without realizing it.