From what the license agreement says MonoTouch apps will clearly not be allowed in the AppStore.
The more interesting question is though, against which framework / apps will they enforce it? They will also have to write automated tests to check if the apps were written natively or not, because the people who approve the apps won't have the time / skills to do it for every single app. These apps won't put a sticker there 'Using MonoTouch / Flash'.
