user uses batch file to disable admin share

Though there may be a technical solution to this, it's really more of a policy/HR issue. Inform that user's manager of the situation as well as the HR department. If they turn a blind eye to the situation, then there's not a whole lot left for you to do. In this situation, they're implicitly condoning his behavior and even if you disabled his ability to turn off the admin share, you'd likely hear about it and be asked to re-enable the user to continue his behavior.

Does this user have administrative privileges? (I'm assuming yes) Short of removing these, I'm not sure how you'd prevent him from disabling the admin share.