Your analogy would stand better if they'd burnt out his kindle, however all they did was negate the existance of the book. Of course, given he had a license for life, whether they returned the price of the book or not, it amounts to theft.
In a case like this, if the copyright holder of the book in question wants it removed like this, it should be up to amazon to agree terms with those that have a copy, as (certainly in this case) just giving them the price back is not really very helpful. Of course, the ideal situation (and how I'd love to see it set up legally) would be the company that produced the ebook being forced to purchase the rights to the book, and amazon forced to pay compensation for their negligence, so they are each in themselves the ones to lose out, rather than all the customers, who've done nothing wrong.