Apologies for being ridiculously late, but if in over 2 years you haven't been able to figure it out, this is a code you can use to delete any stable locations/jump points/planets that exist, including ones created by commands.
runcode SectorEntityToken ent = Global.getSector().getCampaignUI().getCurrentInteractionDialog().getInteractionTarget();
if (ent.getMarket() != null) Global.getSector().getEconomy().removeMarket(ent.getMarket());
ent.getContainingLocation().removeEntity(ent);
You have to be in orbit of them first, though - you can't remotely delete them from across the map.