A better criticism of Jared Diamond's work would be that his work suffers from a lack of primary source evidence: he's not doing experiments or directly synthesizing actual data, he's synthesizing the results of studies. And since there's no objective way to choose which studies are relevant or evaluate the methodologies of different studies, that inevitably introduces his own bias into the process.

That said, I haven't seen any studies contradicting the claim that grains in diet are correlated with tooth decay (which is a smaller claim than the larger claims Diamond makes about health, and which I think the primary studies he cites actually support).

However, that's completely irrelevant to our food choices today. Modern agriculture is quite capable of producing foods which are more similar to foods we subsisted upon pre-agriculture. On an individual level, there's no reason for us to choose to eat grains. I suppose if everyone in society decided all at once to stop eating grains, it would cause problems, but that's unlikely; I think if society slowly shifts toward eating fewer grains, modern agriculture will be capable of adapting.