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It hits the press from time to time that somebody was successful taking down a botnet. We had some success as well with the Waledac Botnet Takedown.
There is actually a good article on What it takes to shut down a botnet. When I was doing some bing-search on the botnet takedowns, I found good work from Microsoft research as well: Your botnet is my botnet: analysis of a botnet takeover.
It is not only about taking down the botnet, it is about going after the criminals and making sure it does not recover.
glad to see you user Microsoft Academic Search to search for papers, let us know if you have more comments about our service.