I suspect that in most cases, once the DDoS attack is ended, nothing happens to the infected PCs, and they remain infected, available for another attack.
Anti-virus programs probably already knew about such a well-distributed malware. There's a chance some users of anti-virus will have the malware automatically removed after the attack, but only if the anti-virus failed to remove it earlier.
The target of the DDoS (i.e. Dyn recently) will focus on mitigating the attack quickly using resources they can control directly. After that is done, they probably do not have an incentive to clean up the 100k or so infected devices around the world.
They cannot practically block the DDoS victims from accessing their system long-term, because most IP addresses rotate frequently, and the complete list of IPs would be very large. Some (but certainly not all) DDoS sources could have been blocked by IP for a short term, but once the attack ceases this would no longer be needed.
I suspect the attacker would eventually cease the attack if it is no longer effective, as that reduces the chances of the infection being discovered/removed, and frees up resources for other attacks. (I could be wrong about this one. Maybe the attack continues as we speak?)
I do not think there is any world-wide or federal agency which will try to get those zombies cleaned up. ISPs certainly will not spend money doing this unless they have to. It's expensive to identify them and would result in a lot of unhappy customers.
Probably the only one who can clean this up without user participation would be the OS vendor.
Windows Update can be used by Microsoft to push a malicious software removal script. Personally, I'm not confident whether will do this or not.
New OSes like iOS, Chrome OS and Android have better management of their corresponding app stores, and have the ability to pull apps that might have participated in a DDoS attack. However, the new OSes are less likely to be infected than classical OSes like Windows, Mac or Linux.
Edit: It turns out many of the infected devices were actually IoT devices such as standalone webcams. Many mfg.s do not have a way to auto-update those devices. Only the device owners could take care of them.