This article by PC Magazine explains the challenges and difficulties in shutting down a botnet

Botnets Takedowns: A Game of Whack-A-Mole?

QUOTE:  Botnet takedowns are exciting. Researchers explain how they’ve infiltrated the shadowy world of botnets and wrested control away from the unknown botmasters who are intent on controlling our computers for their nefarious purposes. Thanks to their technical expertise, our computers are safe again, at least, until the next infection.

On Mar. 26, Microsoft announced Operation B-71, in which its Digital Crimes Unit worked with industry partners and law enforcement to seize over 100 domains and shut down servers used to control a group of Zeus botnets. Kaspersky Lab followed up three days later with its own shutdown story with Crowdstrike and Dell SecureWorks to take over the Kelihos botnet, which may have had 116,000 machines under its control.