This is the key:

>At the end of the play, we're still unclear as to whether she
>made the right decision. But it's the making of that decision,
>and her victory sans evidence, that shakes us up just as much
>as the prospect of a child being molested under our noses.


And regarding this part:

>I'd re-examine the flick. It's easy to get thrown for a loop
>if you immediately think that the priest is innocent... but
>it's not evident in the play that he is, and I'd be surprised
>if Shanley changed that for the movie. Clearly, the actor
>playing the priest is acting in a more sympathetic manner...
>but the sister has doubts for a reason.

The movie is the same way. They actually present a fair amount of ambiguous "facts" throughout the movie that one could use to support either side of the argument. There are certainly no sides taken by the director, he just presents both sides of the coin in a neutral way.