Please take no offense, but there is a bit of fault in your logic.

If someone has access to that one account, why don't they have access to root as well? Most likely they do. Especially if the machine is set up well, so that root is the only user that can get access to that account. At that point don't worry about the perl script or the files that you're working on. Worry about the machine (rm -rf /).

Hoping that the cracker isn't a particular type is about the worst security you can carry, since crackers come in more flavors than unix.

Hope This Helps,
jynx