I have read that there are joints in your neck. One is called pivot joints and I think they can become inflamed(like all other joints) and cause pain and stiffness. So maybe it is joint stiffness from lupus?
Also, perhaps try to sleep differently or use a different pillow. Heating pad might help. I know having a stiff neck hurts and is worrying, so of course see a doctor(maybe ask your rheumy if this is normal) if it keeps continuing and lupus meds aren't helping.
I hope you feel better soon!