YES. And he did it. Think about the events of the movie chronologically, especially the events surrounding Donald being called to the rectory by Father Flynn.
Chronologically, according to Father Flynn, what happens first? Mr. McGuinn catches Donald drinking altar wine. When? Not sure. Mr. McGuinn presumably tells Father Flynn, because Father Flynn certainly finds out about it. Chronologically what happens next? Donald is sitting in class and Sister James gets a call; Father Flynn wants to see Donald in the rectory (we find out later it was about Donald drinking the wine). Donald is acting perfectly fine in class, not drunk (and Sister James says he acted oddly after coming back, not before he left).
Now, does he know why he's being called to the rectory? Well, he certainly knows he got caught, and that it wouldn't end with McGuinn. Father Flynn says he called Donald to talk about drinking the altar wine, so, that talk happens next. Then what? Donald comes back to class acting strangely, with alcohol on his breath. So, if Father Flynn's story about Mr. McGuinn catching Donald is true, this is the second time Donald has drunk altar wine; once when he got caught and a second time, either before he talked to Father Flynn that day or after he talked with Father Flynn.
Either way, it was after he left class because, again, he was not drunk in class. So, are we to believe that Donald stopped off in the sacristy and drank altar wine BEFORE he met with Father Flynn, and showed up for his meeting with Father Flynn drunk? Or are we to believe that Donald actually got drunk on altar wine RIGHT AFTER having a talk with Father Flynn about drinking altar wine? Either option is ludicrous!
Let me make it simpler: Donald got drunk sometime between leaving class and coming back to class. WHEN did he get drunk? Either he got drunk before and showed up for his meeting drunk, or he got drunk after his meeting, before getting back to class. I don't believe this kid would have done either. But he could have gotten drunk during the meeting, and we know why.