Actually, this isn't really a new problem. In fact, it's an FAQ: How can I hide the source for my Perl program?.

Admittedly, you (or in this case your boss) may not be satisfied with the answer in the FAQ. You can find other answers in Protecting Perl Code, Obfuscate my perl code, Obfuscating Perl (on purpose!). (All of which I found by searching for 'hide source' in Super Search.)