Does he distinguish between planners actively consider malaria when siting cities, and people defacto not being near malaria prone sites because the people who were there died/moved away?

Diamond has a tendency to assert things that could be true as true. He draws conclusions from a limited base of facts.

There may be reason to doubt that particular claim. Though it doesn't refute Diamond, David N. Weil, _The Impact of Malaria on African development over the Longue Duree, in Africa's Development in Historical Perspective edited by Emmanuel Akyeampong, Robert H. Bates, Nathan Nunn, James Robinson, gives ample reason to look into it further.

In this chapter, I ask how malaria influenced economic development in Africa in the period before European contact. In particular, I ask whether malaria played a role in holding back African development and whether malaria shaped the geographic pattern of development.

As mentioned previously, another potential channel through which malaria might have affected economic development is through shifting population away from potentially productive areas. Gallup and Sachs give examples of this occurring in Europe. In the context of Africa, I do not know of evidence that particular regions were not settled because of malaria, and there is certainly evidence of of people settling in area of tremendously high malaria transmission. Given that malaria deaths were concentrated among the very young, and that mortality in this group was very high from other causes in any case, it is hard to see how malaria would have had a great influence on settlement patterns.

[...]

As a starting point, it is worth noting that many of the areas with highest malaria ecology and highest prevalence of the sickle cell trait, most notably coastal West Africa, also had the highest levels of economic development by the various measures discussed in Section 3.1. Obviously the lack of correlation between malaria and low development is not firm evidence for a causal link. Those parts of Africa could have been well developed for other reasons, and were it not for malaria might have been more developed still. Nonetheless, simply looking at the locations of development and malaria suggest that malaria was not an insuperable obstacle to economic development.

My more detailed examination of the possible channels through which malaria might have affected economic outcomes also doe not point to a strong role of the disease in holding back economic development. [...] The fact that malaria bulked so large in the view of foreigners may be attributable to their lack of immunity, which Africans acquired as children.

Curiously, I just noted that Weil cites Guns, Germs, and Steel in the references section, though it's not clear exactly what he's referring to.

One might try looking for relevant data in McEvedy, Colin and Richard Jones. (1978). Atlas of World Population History to correlate populations with their specific microclimates. I don't have access to it, and I don't know whether any useful data might be in there.

Woof, you may have opened a can of worms referencing Jared Diamond on this subreddit; he's kind of a lightningrod for tension for a lot of reasons. On the one hand, he has the academic background and published (and peer-reviewed) papers to make him a legitimate academic. On the other hand, the commercial nature of Diamond's book (especially Guns, Germs, and Steel) with its attendant lack of in-text citations makes his work not academically-sound for history purists.

Part of the problem, as I am sure you've sussed out from the comments below, is that without specific in-text citations, we never really get a bead on where he is getting his information, which is at best problematic.

All authors, academic and otherwise, use speculation to fill in the gaps of their research. That's not really a bad thing, per se, but coupled with Diamond's (more likely his editors') decision to not have in-text citation, leads many academics to call foul.

Add to this the "generalist vs. specialist" tension in history as a discipline. Diamond comes across as a super-generalists in his magnum opus precisely because of the scope of his book; all of human history over all the major continents. It is a LOT to work with and, by necessity, elides a lot of context, nuance, and more subtle study. Specialists, on the other hand, can delve very, very deeply into a topic to the point where they will not only be astoundingly well-informed on that specific subject, but also that they'll be blinded to the bigger picture or wider context. Basically, generalists argue that the really minute stuff gets in the way of the wider story while specialists say that ignoring the small stuff makes the narrative incomplete. If you think the treatment of Diamond is harsh here, you should see some of the nasty back-and-forth that happens in peer-reviewed journals; nothing bloodier than a geek fight.

The upshot for your particular question is this; he seems to be offering speculation which many take as fact (due to the weak citation) at least in this aspect. I'd recommend following some of the excellent posts and links of the experts here - they are mostly specialists, so will know what they're talking about on this particular topic.

Don't have the book in front of me, but from the transcript of the PBS Documentary based on the book:

But tropical Africans were combating malaria with more than just antibodies. Their entire civilisation had evolved to help them avoid infection in the first place. They tended to settle in high or dry locations, away from the wet, humid areas where mosquitoes breed. And by living in relatively small communities, spread out over vast areas, Africans could limit the level of malaria transmission.

Just based on this, Diamond does little more than say "evolved" and "tended to", implying it wasn't a concerted conscious effort.

That said, malaria transmission is likely far more related to the dry/wet season, especially on the western coast.

I think I remember reading once that some massive percentage of all human deaths ever has been caused by malaria. IIRC it was half. I dont know if I remember that correctly and/or believe it. Does anyone have insight on that?

Is he talking about a more specific region? What are the population sizes and densities? By away does he mean actually far or simply not on the border of the lake?

The effect would need to be very strong to justify depopulating a nice area and to even be noticeable in small population sizes/densities. Malaria can still thrive in altitudes up to 2000m [1] (although I am aware P. vivax is less virulent) and there aren't a lot of places in Africa where you can move up further than that (which I am sure is something Diamond knows very well). And even though the correlation between distance to large body of water and malaria incidence exists [2], the effect is apparently not reported in monsoon/equatorial climate where rainfall patterns are a strong driver[3].

I am interested in what people with answers instead of more questions will say, but it looks to me that the cost/benefit is not in favor of Diamond's allegations.

[1]doi: 10.1186/1476-072X-8-5

[2]doi:10.1111/j.1365-3156.2007.01878.x

[3]doi:10.1186/1475-2875-7-156