Never thought about this before.......some ideas.....
First - don't put it where they can get it. Sorry, I know that is an obvious one, but valid none the less. I guess this is kind of hard to do if the code is going on their server.
Second - You could bundle the code into executables with perl2exe or activestate's perlApp, but using those can be a little bit of a pain.
Third - If you don't need the programs to be executable ( just storing them ) you could come up with a simple map for a-z, A-Z, 0-1, and some punctuation and convert the text. Save the converted versions. Just don't loose your key.
I'll be interested to see other responses.
[sig]<p> <br><a href=mailto: > </a><br><a href= > </a><br> keep the rudder amid ship and beware the odd typo[/sig]