What is negative or harsh about Gems, Germs, and Steel?
It is difficult to characterize any part of this book as harsh or negative because it does not criticize anyone or blame anyone for the problems that face certain societies today. You could say that it is harsh because it provides no hope for what a society could do today to improve itself. If societies' success is not due to anything like culture, it is not possible for a society to change its culture to become more successful. However, that sort of prescription is not what Diamond is trying to do in this book.
I suppose that you could say that the book is not very sympathetic. It does not show a great deal of pity for the Incas or any of the other groups that ended up as "have-nots." But once again, that is not what Diamond is trying to do. He is trying to explain things, not pass moral judgements on what happened.
Overall, then, I do not see anything that seems negative to me in this book, though there are things that others might see that way.