The Stuxnet worm was clearly a one-shot weapon. Once the flaws in the OS were patched it couldn't spread outside the control system. Clearing it from the control system might be a PITA, likely you have to shut everything down, but the process is routine. Once the OS is patched and the control system purged Stuxnet is gone. It will remain as a historical footnote. Possibly as a pet worm in someone's sandbox system where they can study and admire it.

The take away is that you don't connect critical systems to public networks. If there is any connection outside the system it is inherently insecure. Keep your OS and security software updated. Avoid Windows if you are concerned with security.