Describing lab-created genetically-modified "Frankenmeat" as "clean" might be one of those things not looked on favorably in the future... Bill Joy is quite likely right that genetic engineering is probably the most dangerous technology ever created, and the one that almost certainly has the highest probability of killing us all.
It may be the most dangerous of technologies currently on the horizons, but it can also have the biggest payoff - it's not just about things like curing diseases, test tube babies, or selective pathogens - it's also the first stop on the way to building living machines, living materials, and cracking molecular nanotechnology, which life is nothing but.
Compared to factory farmed meat it is most certaly clean. No unnecessary suffering of concious animals and far smaller impact on the environment make it that.
I'm not even sure that clean meat relies on genetic modifications, but even if, so what? There is no reason to believe that targeted changes are more harmfull than random mutations.