My 2 cents into removing non vanilla bases objects and systems....
1. Have nommies developing new weapon of mass destruction
2. Have it suck all objects of the whole system into a "Landfill system" (No JH and JG attached)
3. Pile everything that needs to be emptied into these system
4. Filled with deadly radiation, with oddly arranged planets all over + graveyards of ships and stations + wreck floating.
5. Pilots can blind jump to this system, no way out except dying or jumping out
6 Profit ????