You could harm your dog picking him up by grasping him at the neck, even if it is the scruff of his neck. I'm saddened that you have chosen this physically aggressive method of training after the hitting/throwing incident. Even Cesar Milan, who employs the "alpha roll" has a disclaimer on the the screen about not trying it at home.
I believe you would achieve much greater results much faster using
positive reinforcement training. You and your dog would be much happier too. Right now, you are teaching him to fear you and physical harm. I think you also run the risk of making him aggressive employing these methods.