Oh man, this could be a big issue for Apple. Unless they had access to your source, how could they even know that your application utilizes dynamically loaded code/scripting?

Your application could be: Python -> Jython -> JVM -> compiled iPhone native and Apple cant tell the difference (or could they?).

Also, since everything runs in the same sandbox, Apple would technically not be able to stop people using the JVM with their applications. The JVM itself is not its own application, its just used to translate java byte code to native iPhone code for your application. Again this raises potential issues on how Apple could police that.