How did the Headmaster take charge of the situation?

What situation are you referring to? In ch 5, Swami sheepishly hands his father’s letter to the headmaster, who then walks into the classroom in the middle of Ebenezar deconstructing and discrediting the Bhagavadgita. The teacher swiftly switches topics, switching to lecturing on the Bible, randomly landing at a page in the Bible and reading out loud the Nativity scene. The headmaster interrupts and asks the teacher why he is only at the Nativity at this late point in the semester, so close to the terminal examination. The headmaster tells Swami that he is “here to look after [him]” and that, if an incident should occur again, he should come directly to the headmaster instead of going to his father.