The 1st one is incorrect. Interro-negative form is "Aren ´t you going to take your medicine ? ´ You need to make the contraction auxiliary-negation.
The 2nd one is correct but the meaning is not the same. ARE YOU is affirmative here and the negation is linked with GOING TO making understand that the person does not intend to takie the medicine.
So the 1st one means : I think that you are going to take your médicine, aren ´t you ? In other words : am I wrong ?
The 2nd one means : Don ´t tell me you don ´t want to take your medicine ! or Don ´t tell me uou are decided not to take your medicine !
Is my explanation answering your question ?