I'm pretty sure that's not true – in the UK at least, any work created during a course of employment belongs to the employer. There's nothing in the Copyright, Designs and Patents Act that explicitly defines what 'course of employment' means but a court would certainly consider it valid were the works produced on company time using company equipment.
Yes, they may have rights to this script. But he probably doesn't owe them any documentation and certainly not training or maintenance. Depending on situation, he may still be able to get something from it and probably he should if they didn't want him to automate that and didn't pay him a real programmer's salary.
If you offer to automate something and the employer says "no, don't mess with our system; it works for us", then automating it behind their backs might not be a work for hire even though it's clearly work-related. This even sounds like the author was being treated more like an independent contractor than an employee.
