This program hasn't even started yet and she's already trying to hold it over a child's head? I'm sorry but I just think that is absurd. Maybe I'm misunderstanding.
Also, if the program expectation is responsibility it seems to me that would extend only to the assignments for that program, unless there is some specific written rule that you should have been notified of beforehand. Otherwise, I wouldn't think she'd have much of a leg to stand on to remove him from this program (please don't tell me she's the only one with decision authority - that is a bad set up, yuck.)
Of course you can't really say most of/any of that to her, the advice from others to chat with her casually about it are better ways to start. I would be irked, however.