Looking through the information on what iOS apps can and can not do, it seems there is more leyway given for apps which are acting as a client for a existing web based game.
I think if you developed Hacker Online as a web based game, since you are already using servers, you would be able to use your iOS app as a client for the web game and include client side scripting, and many of the features you were having problems with including now.
It seems to be as long as you can do it outside the iOS app, they will allow it in the iOS app.
