This uses Cocos2dx, which is c++. Emscripten does not yet support Objective-C. Even if it did, someone would need to write an Objective-C runtime (probably not too hard, especially if you lean on Cappuccino for objj_msgsend). Once that hurdle is cleared, you'd need to source code for UIKit & whatever iOS frameworks you're using. What's more likely is a port of AppKit using Cappuccino components.
"we’ve learned that the successful teams...build on mature (read: “old, creaky”) technologies, because you want to spend time making the game fun, not trying to get the latest and greatest development tool to work."
That, rather painfully, makes a lot of sense. We're 18 months into building an HTML5 game (http://warsocial.com) using rails, node.js, redis, angular.js and a bunch of other 'latest and greatest' technologies. We probably could have gotten where we are now in a couple months if we had just gone with Flash + PHP or something, and put the rest of our time into making the game better.
New technology will always cripple a game project, yeah. The core task of actually prototyping and iterating on mechanics and design until you have something fun is just incredibly expensive and difficult; layering difficult technological challenges on top just makes it worse.
I like to prototype with a scripting language (LUA usually with ZeroBrane) and either Inkscape and/or Blender until mechanics / game design is fun. Not always but sometimes it needs to be almost completely rewritten to C++ or something else more performant than LUA (Cocos2D-x, Monkey language, Unity, Blender gamekit are my among my chosen poisons). Luckily most environments can be extended with a LUA engine, even if it's not supported natively.