I am sure something could be worked out, provided the botnet has enough hashing power to be worth accommodating. About how many connections are we talking about, at what average hashing rate each? I wouldn't expect anyone already running methods of accommodating botnets will want to publicise their details so I expect negotiations would typically be on a botnet by botnet basis and of course you'd have to take the chance that it is a honeypot operation looking to find botnets...

-MarkM-