What is Father Flynn's reaction to the surprise interrogation in Sister Aloysius's office?

Father Flynn feels uncomfortable and explains that he merely talked with Donald Miller about private matters. After Sister Aloysius presses him for more information, Father Flynn attempts to leave the office in a huff. However, before he gets to the door, the nuns explain that there was alcohol on Donald’s breath. Father Flynn replies that the women should have “left the matter alone,” as he was already aware that Donald was caught drinking altar wine and doesn’t want the boy to be reprimanded. Sister James is quick to believe the priest’s explanation, but Sister Aloysius is far more skeptical. Before leaving the office to write his sermon on intolerance, Father Flynn tells the nuns that he is displeased with how they handled the situation.