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How do you respond to shutting down a botnet?

Traenk wonders about shutting down botnets...

Let me begin by stating I think botnets are a terrible problem on the Internet.  It's astounding how much computing power is generated just getting bits and pieces of processing power from otherwise bored computers.  I'm just wondering what are the criteria for crushing a botnet?

Years ago, I was asked to comment on the Seti program, that bit of software that would analyze data for signs of alien contact, in between rounds of game level loading, or so we might hope. 

Sure, Seti is a worthy cause, and their application represents one of the earliest glimpses at what is possible with their 'inverted cloud' design.  But what exactly was it?  What can get put into place if/when hackers find a hole in the Seti application?

Nope, we'd have no Seti, fearing what might happen.  As I read of the break up of a botnet, I wondered.  Who makes the rules?  If I and 50 thousand other users consent to using both our bandwidth and our computers to breaking some cheesy encryption algorithm, as a demonstration of weaknesses in some modern ciphers, are we a 'botnet' needing to be snapped apart?

Certainly, illegal activity must be prevented before it begins.  What if the distributed processing is some task that isn't illegal, immoral, or illicit? 

Processing is world-wide and involves international laws and precepts.  I believe the Internet and its borderless scope makes ethics difficult.