3.3.2 An Internal Use Application may not download or install executable code. Interpreted code may only be used in an Application if all scripts, code and interpreters are packaged in the Application and not downloaded. The only exception to the foregoing is scripts and code downloaded and run by Apple's built-in WebKit framework.

I take this to mean that the javascript has to be downloaded by the webkit/uiwebview as part of an web page and you can't supply the javascript externally if you get if off the network.. There is a lot of confusion online on this point(some people disagree) but that is my understanding.