The Pizarro incident was one example to illustrate a principle. I think Magellan, Malacca, etc. are the exceptions to the general rule. As a whole the European colonization of Africa, the Americas, and Australia is overwhelming proof of that. I'm not saying they were right to colonize as they did, but they were definitely able to.
And racist? Diamond goes to great lengths to specifically refute the racist idea of history. I quote, "the striking differences in the peoples of the different continents have been due not to innate differences in the peoples themselves but to differences in their environments. I expect that if the populations of Aboriginal Australia and Eurasia could have been interchanged during the Late Pleistocene, the original Aboriginal Australians would now be the ones occupying most of the Americas and Australia, as well as Eurasia, while the original Aboriginal Eurasians would be the ones now reduced to downtrodden population fragments in Australia." (Guns, Germs, and Steel, p. 405 of the 1999 Norton printing.)
I'm not trying to get into an argument, but am curious as to what you consider pseudoresearch and half-truths.