A patient (who is competent to make decisions) always has a right to refuse treatment. It sounds like what the doctor is doing is simply protecting himself or herself against
a liability claim by getting written documentation that your husband's failure to follow a particular course of treatment is contrary to the doctor's medical advice. But this has nothing to do with Medicare coverage.
The question of whether Medicare will cover future medical care your husband receives depends entirely on whether that new care is prescribed by a physician (this doctor or someone else) and is considered by Medicare to be "medically necessary." Whether your husband had previously refused other treatment should have nothing to do with that.