[WS:] It is an interesting story. However, I strongly suspect that sympathies with the two sides in your story depend solely on one's view on public displays of patriotism. If one is against it, one will side with you, if one supports it, one will side with the teachers.
Try a little thought experiment and imagine, if you will, that the behavior in question is not saluting the flag but, say, displaying sexist gang symbols on his t-shirt or using mobile phones in the classroom - which are common problems in schools today. Do you think that the teacher sending the student home to change his gang garb or confiscating his mobile and asking the parents to pick it still an unjustified act of arbitrary disciplinarianism? I definitely do not - in fact I support the teacher trying to discipline the disruptive student in such situations.
The problem that you are hinting at has nothing to do with critical thinking on either side. I do not want to speak of your son personally, of course, but in most cases students who disrupt instruction do so because of the groupthink rather than critical thinking - that is because disruptive behavior will earn them respect among their peers. Likewise, teachers' disciplining that behavior has more to do with being respected by their peers than with any pedagogical purpose.
A case in point. In an altercation between two male students in the school where my wife teaches, one student accidentally knocked down a female teacher, who got slightly injured. Initially, both parties acknowledged it was an accident - the student apologized and the teacher said it was no problem and did not press any charges (in fact, she did not follow the school rules as she tried to intervene in the altercation.) However, as the time passed by, both parties came under the peer pressure to change the story. Other students commended the offender, implying that he did on purpose, so he changed his story and started boasting that he did it on purpose. Other teachers demanded that the injured teacher press charges out of solidarity to other teachers. The otherwise minor incident quickly escalated to a major conflict.
So the problem is not the lack of critical thinking or disciplining future labor force -as you imply, but rather groupthink and rigidity on both sides (teachers vs.students and their parents) who tend to get confrontational and escalate the situation instead of de-escalating it. An example of the latter in your son's situation would be the teacher calling a meeting with you and your son and say something like "I understand and respect your feelings about the pledge, but please understand that others find it offensive, so let us work on a mutually satisfactory solution, for example your son going to the support room when the pledge is being recited and coming back when the instruction begins."
My point is that most conflict situations can be de-escalated and resolved by the use of proper social skills and bona fide negotiations. The problem is that we live in a "stand-your-ground" society that encourages people to defend their "honor" "respect" "status" and similar nonsense instead of taking a step back and trying to find a mutually satisfactory solution to a conflicting situation. So it is not really a 'school problem' but as usually a 'social problem' - one of macho posturing, cockiness and poor social skills under the rubric of 'individualism." -- Wojtek
"An anarchist is a neoliberal without money."