Sigh…
The menahel may feel that it is not appropriate for a student to talk back to a rebbi, regardless of circumstance. (It’s certainly not a student’s place to make a judgment about whether a rebbi deserves his position or the respect due one in that position.)
Whether it is reasonable to expect of a verbally abused
student not to respond is a different matter. Those who
“hear their shame but do not answer” are considered to be
on a high level…
So, I would say that your son should apologize, assuming he is willing.
This will get him back into class without further conflict.
Once that is achieved, if there is a problem with the way the rebbi addresses your son, go ahead and take it up with the menahel,
but I think it would be best not to mix the two issues
if possible (or, if you already think of it as one issue, to split it).