Unless he had leprosy or meth sores or something, I wouldn’t care.
I’m not concerned about the bacteria on his skin; I just don’t want anyone else’s skin flakes in my coffee. If they’re in there from floating around in the air and I don’t know about it, I’m not concerned about it. I don’t need to see someone scratching right over my cup, though - there’s a whole world of places they can scratch that isn’t right over my cup.
Scratching an itch is often one of those things that we do without thinking. I’m certain that he wasn’t aware of what he was doing. I’d mention it and ask for another cup. I don’t anticipate that he would object at all. He probably doesn’t wouldn’t be comfortable seeing someone else depositing dead skin in his own food.
It’s a cup of coffee. It costs under a nickel to make, they can afford the loss. There may be some reluctance to toss out a saucerful of Beluga caviar, but not coffee.