Although Guns, Germs, and Steel is a book about the impact of geography on history, Diamond does not deny that ideas have an impact on history. Diamond clearly believes that ideas can have an impact. For example, on p. 366, he says that
developments in Eurasia were also accelerated by the easier diffusion of animals, plants, ideas, technology, and people in Eurasia than in the Americas.
By saying this, Diamond is making it clear that ideas do matter just as much as any of the other things that can diffuse from place to place. He also includes an entire chapter on the development of systems of writing (which is an idea) and one on systems of societal organization (also an idea). Clearly, then, ideas matter even to Diamond.
What Diamond is saying in this book is that superior ideas are not tied to racial or cultural factors. He is saying that Europeans do/did not come up with better ideas because they are racially or culturally better. All people had and have the same ability to come up with good ideas. It is just that some people had longer amounts of time to come up with ideas and larger populations to have the good ideas.
If we accept that ideas can have an impact on society, then we need to think about where ideas come from. Diamond does not explicitly tell us where ideas come from. Presumably, ideas simply come from human beings at relatively random intervals. They are a product of our innate intelligence. People have ideas simply because they are people.
Diamond acknowledges that ideas are important. However, he would most likely say that having good ideas (and having them be useful) is tied to good geography. In places where farming developed early, populations grew and there were more people to think of ideas and longer times for them to think. When people randomly came up with good ideas in farming societies, they had other people with whom to discuss them and they had the societal infrastructure needed to put good ideas to good use.
In short, I would argue that ideas clearly have an impact on society and that they simply arise randomly from human brains. This fact does not weaken Diamond’s thesis as it is possible to argue that geographical factors determine where the most ideas would have arisen and where societies would be best placed to make use of those ideas.