Doubt, Indulgence

I think there is something more to be said on the subject of indulgence which I had not followed through with in class.
The scene with the tea and sugar seems to point at a certain amount of indulgence in Father Flynn's character. Three lumps of sugar and long fingernails (which may or may not be a sign of effeminacy, but displays a sign of being both clean and more so a small sort of vanity). Not being Catholic I can only generalize about the accepted behavior of members of the clergy, and it would seem that any sort of indulgence would be unacceptable, or at least there would be a strong attempt to do everything in moderation in order to curb indulgence, even when it comes to something so simple as sugar. It just seems that if Father Flynn lacks that sort of decorum, lacks the reservation and self-control in even the smaller aspects of his life, whether it be in his consumption of sweets or in minor narcissistic tendencies, then he would not hesitate to indulge in other more serious ways.
It seems as if he is also very presumptuous and takes liberties, such as when he sat down in the chair behind Sister Aloysius' desk during the chair scene. He's very sure of him self to the point of being very rude and self-important, marking his place as the superior in the scene and even seeming to disregard Sister Aloysius' own position of power. And upon leaving the scene he does not opt to talk to the monsignor about the situation and settle it in that manner, but instead states that he will suggest that Sister Aloysius take a break from her job. Seems as if there are some power plays going on in Doubt, mostly Father Flynn making a play for power over Sister Aloysius and she in turn trying to circumvent a structured church hierarchy that is will not support her, right or wrong, in order to do what she thinks is right. In one of the last scenes Father Flynn also instigates a private meeting with Sister Aloysius, which is clearly against the rules, and granted I could appreciate a private conversation in order to resolve a conflict betweeen two people, but if he was innocent and had nothing to hide he shouldn't have had a problem with there being a third party present. If we could arguably see all of these as indicators of an abuse of power, then to what extent could Father Flynn take that abuse of power, especially over those who are most vulnerable to his influence?
At first I was like Sister James during the tea scene, relieved that there was a logical explaination for what had happened and quick to accept it. There seemed to be evidence to the contrary later on in the story, especially in regards to Mr. McGinn. Father Flynn said that it was Mr. McGinn who had caught Donald Muller with the wine, but it was later reveiled that Mr. McGinn had known that the boy had been drinking, but had not caught him in the act nor did he know the exact circumstances as to how he had acquired the wine. So this doesn't do anything to prove Father Flynn's innocence. While I agree that Sister Aloysius is a hard-ass and had taken some great liberties and stepped out of bounds in order to weasel him out, I don't feel that she was entirely out of line, she did what she had to do and that meant breaking some of the rules of the church and general social rules. As far as I'm concerned she called his bluff, if he was trully innocent he wouldn't have accepted to leave so readily faced with the knowledge (which was a lie) that Sister Aloysius knew something about his past, had confirmed it with other nuns at other parishes, which was breaking the rules, but while he pointed his finger at that he broke rather quickly. No, Sister Aloysius was unable to really stop him in the end and he moved on to become pastor at another parish, but she got him out of her school and away from those children which was her immediate concern. If faced with the choice it is better to damage his reputation in order to protect the children. But remember, it never really got out and she never managed to question his reputation to a wider audience. He wound up safe.