I think that scruffing is appropriate for severe offenses, and pinning or forcefully restraining a dog can be very effective, particularly with younger pups. But you have to use it with consideration, both in type and strength, and you have to use it precisely, and you have to use it predictably. And that's with what I would consider a 'normal' dog -- not an insanely reactive one like the dog in the above video.
But the important thing is that significant physical punishment shouldn't be used unless it's the only recourse due to practical constraints (the dog has to learn its lesson NOW or it's in/being a danger) or because you've exhausted the reasonable other options. You also have to mark it properly so that the dog understands that punishment will come when it performs this action, but learns that punishment only comes when it has been marked, and so gets a chance to check its action.
I think that the age of the dog also matters significantly. Pups usually respond pretty well to a stern voice and restraint: grabbing them by the nape of the neck and forcing them down or away and holding them immobile works particularly well, since they're used to getting mouthed like this by their mom. However, if the dog was reactive and older, or particularly handler-sensitive, or a host of other things, I wouldn't feel comfortable doing this, and would probably prefer an e-collar or something similar. But puppies? Works just fine. Immediately rewarding them for calming down/submitting/relenting also helps reinforce the lesson and reinforce that while engaging in a behavior brings a negative stimulus, not engaging in it brings a positive one -and- the cessation of the negative stimulus.
Also, in this case, I'm not entirely sure that 'punishment' is what's happening here -- forced habituation is more like it. Caesar actually uses quite a few behavioral techniques that seem sort of ridiculous to laypeople. One of these is that it's hard to maintain a conditioned response if you're not allowed to actually perform that response. This shows both at the point where he moves the dog's tail out from between its legs and when he pins the dog down and doesn't let it move. The dog learns that a: what it's doing isn't working, b: this guy isn't doing anything that's actually hurting me, and (hopefully) c: god, this is exhausting, if he does this every time I do that, I'll just sit there instead. Also, by not letting the dog get all hyped up and engage in the behaviors its been engaging in, it helps wind the dog down.