Given the problems these botnets cause to everyone, and not just the suckers who have an infected computer, I f think remotely neutering them may be the best option.
Sure it is going to upset the owners, but disabling internet access and forcing them to take it to someone who knows enough to fix it is a kindness in the long run. Yes, it might be an act of questionable legality in some places, but the last time I read a Windows EULA it allows them to 'break' it for DRM reasons so I can't see much reason they can't do it for reasons of it causing trouble world-wide.
Now if said computers are doing something safety-critical there is a problem but:
1) Windows is not certified for that by the EULA
2) Whoever is in charge of the system should be getting a kicking for not having cleaned it up already.