What point of the book related to spread of disease do you have a problem with specifically? Every prominent book has critics, especially in non-hard sciences, that doesn't mean the book is wrong generally. As a general probabilistic diffusion framework, it makes total sense to me.
It's the other points being made, one could get the idea that germs made Europeans stronger, but on the other hand, less germs could give a civilization a developmental edge. Europe lost probably hundreds of years of progress to the Black Death.
> less germs could give a civilization a developmental edge.
Interesting idea, but the way I see it, disease is a cost of civilization in a way. The reasons that there was more disease in Eurasia are also the reasons that caused civilization to progress faster there to begin with. I'm not sure you could have your cake and eat it too.
> Europe lost probably hundreds of years of progress to the Black Death.
Based on what I've read about the Black Death, I don't think that's the case. Unlike the fall of the Roman empire, there wasn't a collapse of civilization despite the devastation caused by it: technological and engineering knowledge was not lost in the process. Some argue that the Black Death was actually benefitial in some ways. There was a big population boom leading up to it, but afterwards the survivors had a better economic situation, and more leverage against nobles resulting in the power shifting more towards farmers and other workers.