Being “dun l’kaf zechus” goes for the boy AND the Menhael.
1. Maybe he IS a good boy.
2. Maybe he isn’t.
3. Maybe he was warned.
4. Maybe he wasn’t.
5. Maybe he shouldn’t need to be warned. (chassidish, or black hat etc…)
6. Maybe there are extenuating circumstances in favor of the boy.
7. Maybe there are extenuating circumstances that the Menahel had to take into consideration.
And last, but definitely NOT least:
Sometimes it’s actually best for the student to be thrown out!
Maybe it isn’t about his short term reputation, but about learning there are consequences to one’s actions in life. Giving him a “ride” now, might just push underlying problems down the road, and the Menahel (maybe even asking Da’as Torah? gasp!) had to do, what he had to do.
Letting him learn this lesson now, might save him a lot of grief and issues later on in life. The Menahel doesn’t have to hate someone to throw him out. He might have to LOVE AND CARE for him.
Unless you heard from both the Menahel and the boy FIRST HAND, this is all kinda ridiculous at best, and loshon horah (if anyone reveals the name of the boy, girl, or school) at worst.