After #1872876: Turn role permission assignments into configuration. role permission assignments are no longer cleaned up when the module providing the permission is uninstalled.
After #1199946: Disabled modules are broken beyond repair so the "disable" functionality needs to be removed this will be possible to implement in a sane way.
Opening this postponed, it's a new release blocker, but a smaller release blocker than converting everything to CMI which the user permissions issue blocks.