It's in the NBC footage that you see the guy nodding. I stopped it mid-nod.
So, what I figure is that they were planning in advance to do the penguin swarm around Bookhout after the shot to keep him out of view, and the guy nodding was probably signalling the others to get ready. Remember the Seinfeld episode in which the bookstore detective gets on the phone and says "Swarm, swarm swarm" to the other agents?
Well, that's what this was. They were going to swarm Bookhout.
How ridiculous is that. In that situation, police would be swift to handcuff the guy, but here, instead, they cover his head with something and then dance him into the building.
Here's the nod in action, courtesy of the Wizard.