Are we all sure this is true? Harper barely ran out of the box on that play. Are you sympathizing with him or are you absolutely certain that everyone was basically strolling out of the box?
I think what Harper did was something we see from players all the time.
If Williams just wanted to make a point, he could have given Harper a stern talking to considering Harper is busting his ass 99.9% of the time. Keeps it out of the public/media light, no one has to answer questions about it, gets the point across.
Instead, he decided to make a spectacle of it and hurt his team's chances to win in the process. Makes him come across as a tough guy and that's the persona he's been pushing publicly since he got hired.
The biggest part of a manager's job is managing people. Does Harper seem like the kind of person who needs to be benched to understand that he should hustle every play? No. Williams has to have each and every player's trust that he's going to help them play their best every single day. Maybe this blows over and Harper gets it and moves on. But maybe part of the side effect of this is that Harper doesn't trust Williams as much after today. Who knows.
I think Williams totally mishandled this situation.
edit: also, it's funny that this comes up after everyone basically telling Harper last season that he needs to not play as hard.