“To throw out as a punishment is certainly inexcusable. The job of the yeshiva is to educate, not punish. There is a very, very small role for punishment in yeshiva, and only if it is part of the education.”
You live in fairy tale land. The job of Mesivta is to train them for the real world. Punishment is part of education; they can’t be acting like wild animals and disrespecting their superiors if they’re ever going to amount to anything.
What would be your solution if a boy beat up another boy? Teach him math? Teach him more gemara?
If a kid threatens the well-being or education of everyone around him, he has to be thrown out. The needs of the many outweigh the needs of the few.