Yup, sys.exit().
I’m pretty sure ShowBase has got its exitfunc registered in python’s atexit or something similar – so sys.exit should pretty much take care of everything.
EDIT: oh, I see you want to keep python running. That would be only possible if you’d destroy the taskmanager, to close down the run() call. Check ShowBase.py in the direct/src/showbase/ dir to see what things ShowBase initiates, and see what command shuts what down.