Me too. The problem as I see it is that humans were not present in large enough numbers to pass these diseases on over such a large area -- it breaks down for the same reason that he gives for the over-hunting hypothesis.
Not that it's completely out of line, however: the American Indians were practically wiped out within a few decades by various "pox" diseases.
Maybe the disease can be carried by a native North American bird that pecks at dung piles dropped by giant ground sloths. The bird then passes the disease to other giant ground sloths, and eventually they all get the disease.
I know it's difficult to think about such a complex process as a multi-species epidemic, but it happens. The best studied system involves human beings, pigs and birds, all living in China. They pass influenza back and forth, species to species, and every now and then create killer flu.
Re-read the entire article - slowly this time!