Of course he didn't, the whole point of the movie is that she's blaming him for something he didn't do, it's clear she has no evidence whatsoever and he's been a good teacher and a friend, movie is about they're relationship and Streep's character having doubt in God, that's where that title comes from, she forces everyone around her to fallow every rule and mockingly speaks of people who have lost faith when after all the years living as a nun she has doubt. Notice the differences between dinner scenes in the movie, her dislike for straying from tradition? Nuns controlled and quiet, priests having fun and laughing, this is the difference between characters and it's repeated in long hand nails monologue, Hoffman's character doesn't care about such small things, same as with wine, it's just a little wine, what could it hurt? But for Streeps character that's breaking the rules, she hates that and she hates that Hoffman's character is more well like by people while he is also not fallowing every rule and in higher position, how can that be fair? She is a better person and a more devoted follower in her mind, and yet she is in a lower position more disliked. She was not the hero here, movie by the way never even explores child's and priests relationships, it's all Streep's character trying to get as much dirt on Hoffman's character as possible and refusing to believe that he didn't do it even though everyone keeps telling her "no".