When I worked in a chiropractors office we often dealt with medicare declining payments. They deemed most things medically unnecessary. (Essentially the same thing as saying it wasn't an emergency.) The doctors would have to code their bill differently, and resend. When you talk with medicare, see if a letter would help. We often faxed letters from the doctor, describing the need for a service.
I worked with insurance 4 yeas ago, so I understand it could work differently now. This is how medicare and supplemental worked for us. Things can get murky when you are dealing with supplemental insurance. They pick up the remainders of what medicare doesn't monetarily cover. However, they won't pick up services or procedures medicare refuse. (I hope that made sense!!) If medicare is being billed first and they ultimately refuse to pay, Health Net would not pick it up. However, medicare will (if they deem it necessary) pick up things Health Net won't cover. It all depends on the need. It has to be seen as needed, or you are kind of up the creek. The doctor should help you clarify that with medicare. Ultimately, you followed doctor's orders. Most likely, this can be totally rectified with a letter from the doctor, or documentation of orders. That's usually all they need.
I meant to add, that I'm very sorry about your loss. Insurance companies do not allow for grieving time, and it's just awful.