I think OP has a good point actually.

The numbers are so enormous that using 100,000+ cpu's would have massive impact on difficulty, forcing mining costs up. Then there is the small percentage of zombie machines that will have a descent graphics card or two that can be put to use. Mining clients are well suited to the botnet paradigm and can be easily integrated.

I guess the question will be whether botnet owners want to do something quite so brazen.