3.3.2 An 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.
The rule was however enforced. My own app was pulled for it a year ago for embedding an little tiny Lua interpreter for handling a few game logic changes.The question is still interpreted code that is not included with the app but written by the user in the app. I used to work for TI programming graphing calculators a couple jobs back. I always wondered if we could do a port of one of the later generation calculators to iPhone but I always stopped at TI-Basic or if our CAS engine could be considered an interpretor. Now given the rule change, would user entered code still be considered against the rules. It wouldn't be code shipped with the app... but still.
(And for anyone who thinks I'm splitting hairs: The line between "document" and "program" really is fuzzy. For example, Little Big Planet's game engine turns out to be Turing-complete, so you can build a working computer in the level editor out of game objects. See here for more: http://forums.xkcd.com/viewtopic.php?f=12&t=57034 )
...but it's still violating the iOS developer agreement. Specifically the no interpreter rule except those provided by Apple. They probably didn't notice but blogging about it may get the apps pulled.
Take it from someone that has been on Apple's bad side: this is a bad idea and will probably get you pulled. They also don't like braggers that figured out ways around the rules.
I've dealt with these things. There are few options though. Compiling to native (in a AOT style) is one way, (ala MonoTouch and Adobe's Flash Convert tools). The other is just embedding a UIWebView somewhere (even if it's not visible) and IPCing over stringByEvaluatingJavaScriptFromString and URL change notifications.