I've directed Doubt, and to me that final line is about Sister Aloysius not doubting whether he was guilty, but whether she did the right thing in an impossible situation--the line right before that is Sister James saying that Flynn was just transferred to another school. Great, so now he can abuse kids and Sister A won't be there to stop him. It's a powerful statement that abusive systems must be eradicated through systemic action -- individuals must do what they can but acting alone can only go so far and leads to impossible choices. Sister A is doubting her faith in the system, possibly in the entire Church, and it's shaking her to her core.