In Doubt, doesn't the nun realize that all she's really done in getting rid of Father Flynn is given him the opportunity to victimize another child at his new place of employment? And if he's innocent, that she's not only bullied an innocent man out of his job, she's left an equally innocent child with no one to look out for him in a hostile learning environment?
Even worse, if Flynn is guilty and had stayed where he was, he would at least know that Sister Aloysius was watching him, and her presence might have scared him into staying away from the children. Moving him somewhere that no one suspects him is the worst possible thing she could do.
Key word is "might." Sister Aloysius made an aggravatingly difficult decision as she had literally no evidence to report to the police, but letting Father Flynn stay and torment Donald, even just mentally and from a distance, would have been unacceptable. She did the only thing she could do in an impossible situation.
If he was, in fact, a child molester, it's essentially guaranteed that he'll find new children at his new school to abuse. Even if she's right, she's protecting Donald from possible abuse by condemning other children to certain abuse. Fridge Horror indeed.
Yes, she did realize all these things. That's one of the meanings that the last line is trying to convey.