If you signed an agreement for MobiPocket to publish your e-books, they are also being sold as Kindle e-books with no additional permission asked for or required. Amazon may not even know how to pay you for the e-books. That is my interpretation of the following MobiPocket Forum thread:
Amazon.com Kindle Books.
Perhaps this only applies to independent authors or small publishers, but it illustrates one reason why Amazon bought MobiPocket.