There should be a way to exclude botnets...
For example, some kind of notification once a week that's hardcoded into the miner. Also, pools should only accept miners that have this notification feature (e.g. by checking the hash of the miner code).
At least, this would ensure that the pools are bot-free...
Further, the original Bitcoin client should have the same feature.

I know that this would only temporarily stop the botnetters, but at least it gives us time to invent a better solution to protect the real Bitcoiners from hordes of Bots.