I don't think there is any direct correlation between MS and hives.
There IS a relationship between hives and the immune system -- the immune systems "job" is to eliminate anything from the "outside" that it perceives as "foreign". That's what happens with MS -- the immune system has gotten confused, thinks the myelin is a "foreign invader", and is trying to eliminate it. Medical scientists are trying to figure out why/how the immune system got confused, and correct that.
Hives, on the other hand, are one way the immune system reacts to foreign invaders that is proper -- the immune system is chasing after something in your system that is "foreign" -- as your doctor said, a virus -- and responding in that way.
But are you SURE you have hives? They usually appear as large swellings, not just small red spots, or a raised red line. At any rate, your doctor should be offering you an antihistamine medication, or sometimes cream, that will treat them.
Otherwise, in this dry weather, if I scratch myself I'll often cause my skin to redden, spots to appear, and they'll itch worse. The skin is a large organ of the body, and with all this bitter cold and heat in the house, I'm flaking all over and itching everywhere.
Here's a website...complete with pictures (ugh!) that describe hives: