If this analysis is correct, there seems to be an easy fix -- just throw the disruptive students out of the classroom, and you can have rather good results with large classrooms too.
The reason this isn't implemented is that children are forced to attend school. If they could get out of classes without consequent punishment, not just one or two 'disruptives' but many students might opt out. A school doesn't have anywhere to keep such a group; classes are in large part make-work to occupy students.
On the other hand, if you punished disruptive students but did so outside of class, the habitual disruptives would spend a lot of time in punishment sessions, and would definitely not learn their lessons / pass end of year exams / etc. Schools in the US* prefer to have everyone barely pass exams, to 80% passing with high scores and 20% failing irretrievably. The failing students' parents have too much political power over the schools.
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Post by fellow LW reader Razib Khan, who many here probably know from the gnxp site or perhaps from his debate with Eliezer.