If your customer is sophisticated enough to edit your scripts, he will not have a hard time decrypting your encrypted or otherwise obfuscated code.

So you better go and see your lawyers and ask them to draft some strong legal text to stop the customer from messing with your code.

One thing I have been thinking of (but only in theory as I lack the knowledge to implement it) is to write a compiled XS-module which would check on a regular basis that the scripts which are part of your project are still the same by comparing their MD5-hash with the original MD5-hash. It would not be too difficult to "hide" that XS-module somewhere in your project and have it called regularly from one of your other routines. If it finds any anomalies, it could throw an exception and stop executing the program.