A film doesn't automatically assume the standpoint of one of its characters. If anything, the film kind of subtly rejects those things by making all of her intolerance very unlikable. Personally, I actually felt the film was closer to endorsing the priest's point of view, by generally making him more likable as a character.

To play the devil's advocate though, can you really blame the sister for pursuing the possibility that one of her students is being molested? There is certainly no hard evidence, but as a principle, wouldn't you have a zero tolerance policy even if there is even a possibility (knowing that there is a history of priests and abuse). Why give the benefit of the doubt (no pun intended...or maybe there is?) if the benefit could lead to severe child abuse?