Would making mock ships work? For example, mock ships would be capital ships that have weapons that blow themselves up the moment they come onto the field. Would ships fight to the death if there's a sufficient number of other ships in its hold?
Or perhaps you can make these mock ships utterly slow, and elongate the map vertically so what you're going to be fighting in the middle of the map is the ship you want to fight one on one with. After you win the fight with that one ship at the centre, these mock ships, while designated as capitals, have a trivial amount of health and shielding. This way you could fight a ship one on one without interference of these mocks ships due to their almost non existent speed, and not have it run away because it detects a host of other "capital ships" on its side on the field.
If it works it can be quite fun releasing a mod about fighting huge monstrosities like a monster of the week type of thing with a small fleet.
