In this book, Jared Diamond is most definitely trying to explain why inequality exists between various peoples of the world. He is trying to explain why Europeans ended up dominating the world, but he is not trying to justify it.
The word “justify” has moral connotations. In other words, it is about what should be, not what is. When you justify something, you explain why it is morally right that that thing should have happened. In this case, if Diamond were justifying inequality, he would be saying why it was morally right for Europeans to dominate the world.
But Diamond explicitly rejects this idea. Justifications of European domination tend to go along racial or cultural lines. They claim that Europeans deserve to dominate because they are racially or culturally better than other people. Diamond rejects this. He says that we need to have a really good way to explain why Europeans have dominated. If we do not, he says (on p. 25 in the paperback edition),
...most people will continue to suspect that the racist biological explanation is correct after all. That seems to me the strongest argument for writing this book.
By saying this, Diamond is disavowing the idea that Europeans deserved to conquer and dominate.
Instead, Diamond is explaining. He is showing why Europeans came to dominate, but he is doing so without saying that their domination was morally justified. He is simply saying that it came about because of geographical chance. This is an explanation, not a justification.