That's what you get when you have a scientist try writing a book that's simultaneously popular science and popular history. And judged as a popular history GGS does get a lot of things wrong and isn't up to the standards historians work to hold up. But on more scientific questions like "why there weren't diseases endemic to the new world that would affect Europeans in the same way that smallpox did to the indigenous populations" it does a good job.
EDIT: Really, the reception to GGS is probably one of the best illustrations of what Thomas Kuhn was talking about in The Structure of Scientific Revolutions about different paradigms having different rules that I can recall seeing in my lifetime.
Mainly "actual historians and anthropologists" on reddit and in related circles. GGS is far less controversial outside these circles and often lauded - also by "actual historians and anthropologists".
Plagues Upon the Earth is maybe even more on point to the plague bit in particular, with the co-evolution of human society and infectious disease over history taking the front stage.
