I really can't decide about Father Flynn

There are so many places in the play where his actions could be taken as both a sign of guilt or frustration. The first example I thought about was in the scene where Sister Aloyisius had her final confrontation with Father Flynn. Up until this scene I had no reason to believe he was guilty of anything save for maybe a bad temper. But then Father Flynn starts begging with Sister Aloysius to not report him. Just this alone was enough to give me a little bit of doubt to Father Flynn's credibility.

The scene we talked about on Wednesday was probably the first example of John Patrick Shanley trying to give the reader or the audience second thoughts about the truth. The thing is, he does it enough to give you a double take of the situation, but not enough for you to necessarily take it as credible evidence. Personally, I didn't pick up on it until the idea was raised in class. I took it as him really not wanting to report Donald Muller and get him kicked out of Altar Boys.

Another I thought of was his solo confrontation with Sister James. Could it be he's trying to really plea with her to see the truth? Or, is it that he's playing on her need for simplicity? I'm not sure. It could reasonably taken either way. There's just no logical, evidence-based way to judge him given the information we're given.

The latest one I've come up with is also during the initial confrontation between Sister James, Sister Aloyisius and Father Flynn. Near the end of the scene, Father Flynn threatens to ensure Sister Aloysius a forced leave of absence. Again it could be taken two ways. Either Father Flynn feels wronged and thinks she should be at least be scolded by one the higher-ups, or he feels she is a threat to his secrecy and wants to get her out of the picture. I'm so confused!

Is there really any clear evidence to either find innocence or guilt in the situation?