That's not a clarifying question, it's a politically loaded statement. That's why the headline only says "suspended for saying illegal alien" and not the whole context because it sounds better that way.
Based on the statement from the teacher and the student. I see nothing political about his statement. It was a clarifying question and the legal term is illegal alien.
Sure, but not "illegal alien who needs a green card," which is needlessly inflammatory.
If a kid raises a hand in class and asks if a historical figure is 7-11 brown or 9/11 brown, it's certainly a clarifying question asking if the person in question is Indian or middle eastern, but it's also incredibly uncalled for and they should be punished.