Just adding my 2 cents. It seems that after reading this part: (e.g., Applications that link to Documented APIs through an intermediary translation or compatibility layer or tool are prohibited) there is nothing to discuss. They have expressed them unambiguously. Not only they are banning MonoTouch and Unity3d, it seems they are also banning Titanium Framework. However, after reading this article, i found myself really confused.
I am not familiar with US laws, but is it legal? I mean, aren't they breaking some anti-monopoly laws?
Besides all of this, i can't understand their motivation. Not only will they partly lose a developers interest, they will also lose a developers respect, i think.