A few people have mentioned that they feel Meryl Streep's character strictly held the priest to the rules and held him to the letter of the law.
I have to disagree.
The letter of the law would have her suppress her suspicions and obediently leave the matter in the hands of her superiors. Here she knowingly breaks the law in order to protect Donald Miller and the other children at the school. She clearly states her belief when she says, "When you take a step to address wrongdoing, you are taking a step away from God, but in his service."
Considering the inaction of others in the movie and in similar real life situations I rather admired her courage in saying, "I will step outside the church if that's what needs to be done, till the door should shut behind me! I will do what needs to be done, though I'm damned to Hell!"
If only more people had even just a fraction of her determination to expose wrongdoing and protect the innocent.
Whether her action was justified is purposely left unclear. If you are certain about whether or not the priest is guilty then I think you have missed the point of the movie.
I'm sure most people will be convinced of the priest's guilt. I was when I first watched the movie.
But, let me offer the following possibility:
Is it possible that Father Flynn is gay? This might have seriously upset his fellow priests and the parishioners in the parishes that he had to leave.
Is it also possible that he doesn't believe, contrary to church doctrine, that homosexuality is a sin? We know that he is an advocate for change within the church. Perhaps he hopes that a progressive church will eventually accept homosexuality as natural.
Could he know that Donald Miller is gay and have told him that it wasn't truly a sin?
I think it's possible though not necessarily likely.