As you know, and I'm sure your supervisor knows, if the IEP says that a study guide or notes are to be provided, then legally they need to be provided.
If the children are not paying attention because they are not taking notes, that is a completely different issue. That is a class management problem.
My son is an auditory learner. He has terrible handwriting and writing is so difficult for him that it takes most of his mental effort to write. If he is taking notes, then he cannot listen. Then he is stuck because the auditory portion of teaching is over. All he has left is his visual mode.
He learns better when all he has to do is fill in a word or two on a note sheet. This keeps them still involved, but does not tax his brainpower significantly (for some it may depending on their disability).
If you are the teacher in the room, and this method is working well for you, plus you are legal, I think the supervisor needs to be politely set straight.
By the way, what is she going to do with the guides????
I can understand that the supervisor wants the info to