sendAllShipsAway isn't really meant for this purpose (I suppose it was invented specifically for the Nova mission.), because the ships leave wormholes. This doesn't give the impression that the system was empty in the first place.
So the method I am asking for here would simply remove all existing entities (probably with the exeption of the main station). In legacy scripting I would suggest removeAllEntities as a method name.
I guess in JavaScript it could get a parameter which determines whether the main station is to be removed as well, or not, or perhaps to be replaced with what. (In interstellar space it would of course make no difference.)