Obfuscation is not a bullet-proof security measure. Anyway, Worklight does not provide this ability built-in, however you can follow the instructions from this IBM Worklight blog post, about obfuscating your application's JavaScript code:
From the blog post:
It is very important to understand that code obfuscation, especially in JavaScript, is a relatively weak security measure. Most modern web debugging tools are smart enough to "prettify" the obfuscated code reverting it to a much more readable (however still not original) format.