M.B.
My first husband who also worked in a hospital. We also had an incident with scabies. Out infant son got them too.
I would complain that my son didn't sleep for long periods and everyone would tell me it was because he was a newborn (if I remember correctly much younger than your son. He was too young to scratch or communicate what was bothering him. I couldn't really notice the "Rash", but we took him in and had it diagnosed. Everyone was treated with Quell (sp?. I washed every washable thing in the house and left on a vacation.
My son was able to nap regularly and was so much more comfortable after the treatment. I say if you got scabies, EVERYONE in the house should have been treated. I would worry about reinfestation.
If your doctor won't prescribe for your son, seek a pediatric dermatologist specialist or just another doctor to help you. I remember just how uncomfortable it was and what a HUGE difference it made in my son's comfort.