>And the film certainly didn't endorse fear and resistance to
>change, nor anything else you said.

Sister Aloysius fears and resists change in the Catholic church. She doesn't like Father Flynn because he uses a ball-point pen and wants to the church choir to sing secular songs during the Christmas performance. Plus, she suspects he may have had an improper relationship with one of altar boys. She collects and fabricates (or implies) evidence against him, confronts him with it and forces him to quit. Which clearly implies he did something wrong while a priest, and is thus a hypocrite, showing how dangerous change can be.

No matter what happened, Sister Aloysius still rules over the school like it's a prison, resisting to bring it into the modern world. But it's all okay because she has private "doubts" like the rest of us. Her actions don't matter, as long as deep down, she's unsure of herself.