I don't think people need to be concerned about Amazon analyzing the material on their Kindles. From what I understand (I'm not an expert on the Kindle by any means), the Kindle is initiating the communication with Amazon via Whispernet. Your Kindle requests synchronization with Amazon's servers, and receives updated information about books that are available to you (most of the time that would be updated when you buy/add a book). In this case your Kindle finds that a book is flagged for deletion, so it deletes the flagged book.
It's not like Amazon is doing a search of your Kindle contents looking for Atlas Shrugged. You (represented by your Kindle) are the one initiating the synch.
A distinction that may or may not make a difference to people's feelings about it, but it is a distinction from what some people seem to be concerned about.
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