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Mono apps are allowed on iOS (eg games based on the Unity3d engine) so it is likely there is way to make Java apps acceptable as well. Oracle seems confident it is going to happen (http://www.infoworld.com/d/application-development/javafx-io...)

As far as I know MonoTouch uses Ahead Of Compilation [1] on iOS. So there is no JIT in compiled binaries.

[1] http://docs.xamarin.com/ios/about/limitations

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