«“This is a prime example of the over-policing of Black students in school.”»
Yup.
«But the substitute teacher was not aware that students are not required to recite the pledge, the school district said,»
This is beside the point. Conflict w/kids is inevitable; handling the conflict WITHOUT bringing in the justice system really is the school’s responsibility.* This isn’t a failure on the part of the sub; it’s a failure on the part of the school system.