I believe the change in policy was that you can now implement VMs/scripting engines but that /all/ of the bytecode/code that will run on them must be packaged within the app (i.e. you can't download more code to run dynamically).
Apple changed/clarified its policy to allow VMs and scripting languages, so long as all the bytecode or script is built into the app you submit for approval. Adding more script after the app is installed on the device is not allowed except for the built-in WebKit Javascript engine.