But the school evidently didn't reprimand the teacher.
And I think we differ about the possible merits of the legal case. The student evidently found it necessary to drop the course mid-year and to continue through a private tutor. If the teacher is creating that hostile an environment, then the failure of the school to reprimand the teacher (or to make sure that the reprimand was effective enough) is indeed actionable.
Which isn't how a typical person would read that sentence, I'm afraid. The use of "you" as a generic that applies to everyone is well-established in English linguistics. (There used to be a pronoun "one" that was used, but that's fallen out of common usage, to the point that you mostly hear that one used as a parody of pretentious academic writing.)
Even so, it's almost certainly actionable to disparage the student's personal religion in that way. The teacher at that point is picking and choosing from among religions in terms of which he supports and which he denigrates. That goes directly into the "sending the wrong message" effect of the Lemon test. If it's the student's "Jesus glasses" that are making him dumb, that's actionable ---- but if it's actually the student's "Bethel Church Baptist and Aluminum Siding Co. glasses" and the teacher is singling out BCBASCo., that's even worse.
And I'm not convinced that the comments would be appropriate in that context.