What about if you have a client that requests that the code stays secure so that competitors can not use or adapt it?

Then tell your customer to pick good passwords for their system.

For example, say a small web design firm has spent the last 4 years building a web marketing business, and has developed systems to track customers, projects, sales, sales leads, etc. They now want to turn this paper system into a Intranet using Perl. But they either don't want their competitors getting the code, or want to sell the code? Wouldn't you want to protect the code source some how?

Yeah, but not by "hiding" the source. You do this by securing the systems the program is run on. In the same way the company keeps secret documents locked up, instead of printing them out rot13 encrypted, and leaving them in the lobby of the building.