I understand that the company told him to not mess with the system, but why not show them that you found a way to automate the process without admitting that he's been using it for a long time.

Maybe I'm too optimistic or naive but after successfully showing them that it works and saves time the conversation could move on to optimizing other tasks and problems the company surely encounters. Instead of letting the guy go I could easily see how they find additional value in him in other areas.