I wonder how many copies of the source walked out the door with those laptops he sold to y'all. ;-)
This sounds to me like he's paying you to chase your tail for six hours. The best way to "protect" the code is to get a lawyer to make sure that all the copyright details are taken care of for the code so that it will be on record as an asset to the company.
If this was a priority for the manager, he made a real bonehead move in having the application written in Perl in the first place. Still, Microsoft and Sun haven't had much luck either "protecting" their code from poor security and disgruntled employees.