Because it's what the students were doing, and she was a student. Japan - especially the school system - has an unhealthy obsession with uniformity, and prefers to eliminate or ignore deviation from the norm. The students are singing, so ALL the students are singing; they don't want to deal with edge cases or individual situations. Naturally for a disable person this is a big problem.
It's also a part of the broader criticism of Japanese teachers (and honestly teachers in general, in my experience) doing everything they can to avoid making a scene or dealing with problems, like the homeroom teacher not addressing the bullying until he was forced to, or sacrificing Shoya so he wouldn't have to address the actual problems with the class.