First, I agree that the Manifesto totally missed the boat when it said that companies need to get out of the way. Smart companies like Dell empower their employees and then act on what those employees, and their customers, tell them. Only a smart, strong company can do that. In my mind, that's why Microsoft has failed to capitalize on the changing nature of media and communications: They empower their employees, but they have grown too ponderous to act.
Second, command and control is definitely something that must stick around. See my first point, above. But command and control is only as good as leadership. Folks who aren't good leaders need to have the courage and intelligence to understand that and step gracefully over to the roles at which they excel.
Finally, I do not think that social media as it currently exists can deliver the ultimate promise of the Cluetrain Manifesto. It's too anarchic. The people with smart answers are often drowned out by the crass jokes, spam and generally poor communicators.