It does not make it a "drug free" nor zero tolerance. It simply reinforces the arbitrary and capricious control doctors have over our bodies and mind. Under that order, it's fine to use meth (a schedule II medication), if you have a "valid" prescription, for abusive definitions of the word valid.
A valid prescription (the little white pads with a doctors signature, not a pot club membership card) for medical marijuana protects you from criminal prosecution, but not from employer drug testing programs. Executive Order 12564, signed in 1986, explicitly makes the federal government a zero tolerance drug free workplace.