To your second point:
If the user is still supposed to be able to execute the Perl script, you can't really protect it. Obfuscate, yes, but securely encrypt, no.

To be clear on the subject of encryption: If you choose a good encryption method and protect the encrypted file(s) with a good key (depending on the method somewhere between 128 and ~8000 bits or so), it doesn't matter if the encryption method is readable to all. Actually, using an open sourced, well known encryption method has a better chance of actually being secure.

If you are new to encryption, you might want to read a few books about it. I personally liked "The Code Book: The Science of Secrecy from Ancient Egypt to Quantum Cryptography" by Simon Singh, ISBN 0-385-49531-5. Also, you might like to read Bruce Schneier's blog and others to keep up to date.