I think it's interesting that a lot of people are taking this as a question in the form of "is this a good idea?" I agree with almost everything said above about how code obfuscation/encryption/"compilation"/etc. is largely a waste of time when it comes to actually protecting anything.

However, I want to point out two things:

1. All of those very good reasons not to hide code mean nothing if your boss requires you to do the hiding. Gripe, complain, present well-reasoned arguments on why it's a bad idea, but at the end of the day, you may still have to do the dirty.
2. Trade secret law requires "due care" from an organization in protecting a secret, or it loses its "trade secret" status. If there's some method in the code that the org wants to keep others from using, it has two choices: patent or obfuscate¹. Since software patents are evil, I'd rather see them obfuscate. Yes, it's broken, but it's probably enough to show that you tried to protect your secret.

In summary, avoid code-hiding techniques whever possible; but, when it's strictly necessary, I say use something as lightweight as possible. I'm curious what kind of performance hit is incurred by using Filter::Decrypt in this context...

{1}: copyright doesn't apply here, as that only protects the particular expression of an idea, not the idea itself.