The administration's response doesn't even pass the smell test of credibility. If the school does not require students to stand for the pledge of allegiance or participate in it, why did the student end up in the office in trouble? Why didn't the principal or some assistant principal simply send him back to class and inform the substitute teacher of the school policy?

The only reasonable explanation for the escalation that led to handcuffs is that somebody in the office was arguing with the boy. Trying to force him to be silent.

Good for him for refusing!