I certainly wouldn't patch class files. I'd just extract the private key, then write a new Java application, utilise the same libraries, and point it at the XML. Boom, decrypted.
Is changing a text file a little easier? Perhaps. But extracting the private key is only slightly more work, and the benefits of being able to debug are worth it since the security arguments are pretty weak borderline non-existent.
If you're really paranoid about this just hash log4j.properties and check it on startup. Then crash out with "corrupted log4j.properties, please reinstall" if it has been modified.