Whenever I'm trying to learn an idiom in a foreign language, I think of the literal parts that make up the idiom. Sometimes that can lead you to remember the abstract meaning of the idiom better. In this case, it's fairly straightforward and I think my method will work here.
Literally, "to look past something" means "to look beyond something", seeing over or around it. Maybe you're looking over a mountain and you see the sea.
But in your example sentence, the teacher is doing something less concrete. Your sentence brings in a question of morality.
You might say instead: "''The teacher chose to ignore the student asking the question to the empty desk at the back of the classroom.'' Not as exact, but it conveys roughly the same meaning.
She's literally "looking past" (looking anywhere but at) the student because she wants to block him out of her mind, for he is unpleasant to her. But more abstractly, she's "looking past" his actions, because they don't jive with her definition of normal or acceptable.
EXAMPLES:
1. The girl looked past her brother's destroying of the hidden den, because he was touched in the head anyways.
2. The boy was a weird sort, and he looked past the outside of a person - he much preferred their inside, because he had always been a bit different.
3. The man looked past his son's faults, because the boy was his son, after all.
Let me know if you have any questions.