My father with Alzheimer's insists on controlling my mother's strong medications. How can we legally make sure that she is getting the right medications?

Sounds like your Mom and Dad both need some assistive care, be it family, or paid help. Someone who has Alzheimer's should not be administering prescriptions to anyone else, or controlling them. Even if he throws a tantrum, it is best to remind him that he has been diagnosed with Alzheimer's (if he still remembers that) and tell him that someone will be assisting him and your Mom with that care function. Best to not wait before he poses a health danger to your Mom's health, or to himself, as he could just as easily think he needs to take some of your Mom's medications, or he may hide them somewhere and forget where, leaving your Mom in a compromised health situation.