I'm not too worried about Apple blocking the Kindle app. Ultimately Apple is more interested in selling hardware than in selling content or software; e.g. Apple made nearly $8 billion in revenues from the iPhone and iPod, and less than $1 billion from everything in the iTunes store.
Since a Kindle iPad app makes the iPad more useful, they really don't have much reason to block it. Same with Pandora, which indirectly competes against iTunes; but since it sells more iPhones, why block it?
That said, this is one benefit to an open platform like Android, as you do not have a nanny telling you what apps you can and can't officially run on your device.
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