Found a solution.
Forced a cleanup before Python starts tearing down the logging module.

Import this library into the code:

import atexit

and add this at the end of the code:

def cleanup():
    plc.disconnect()
    plc.destroy()

atexit.register(cleanup)

After executing the script, the original error doesn't occur, and now we can remove the atexit portion of the code and execute like normal.