I wish I had seen the play. I left the movie feeling relatively certain of the priest's guilt, but it's certainly possible that I was projecting my own bias into the film. I certainly didn't pick up any doubt from the nun as to the role the priest had played. At the end she said something to the effect of "his resignation was his confession."
A friend and I were debating this point a few weeks ago. He thought the movie was much more open-ended than I did. To me, it was more about the fallacy of judging a book by its cover. The nun appeared to be bitter and mean-spirited, but in the end she had the boy's interests in mind, even if she was moved to protect the boy more out of a desire to strictly enforce the rules than any particular interest in the boy's well-being. On the other hand, the priest appeared to be interested in the boy's welfare, but only because of his unnatural desires. In the process of ensuring that the rules were followed, the nun lost her faith in the church. Of course, this is one possible interpretation, but it looks like the movie is certainly open to various others.