Actually, 3rd party browsers are now allowed on the App Store, with a few restrictions. Previous, section 3.3.2 of the developer agreement prevented the downloading and running of any code, except for JavaScript running inside iOS's JavaScriptCore. But the June 5th agreement allows any language and interpreter.
There are two limitations. The system makes it impossible to run unsigned code, so JIT compilation is out. Also, an app can't establish its own app store, so Google would have to get special permission for the Chrome Web Store.
That's in the App Store Review Guidelines, not the Apple Developer Program License Agreement. But that is a good point.
However, Opera Mini has a “Mini mode”, where the parsing and JavaScript execution is done on Opera's server, which then compresses the data and sends it to the phone for display. In this mode, it does not use the WebKit framework. Opera Mini has been on the App Store since 2010.
I wonder if section 2.5.6 applies to apps that display web pages as one function among many, and not to web browsers. Maybe Apple figures that if the user hits a “Web Page” button in some app, they expect it to work just like Safari, but if they download Chrome, Firefox, or Opera Mini, they actually want the web browser to be different from Safari. But I haven't researched this yet.
