I would say that Diamond calls this a “collision” for two reasons. To see why this is so, let us think about what a “collision” is. A collision occurs when two bodies run into each other. At least one of them has to be moving at the time. A collision typically has destructive results. The “collision at Cajamarca” embodied both of these things.
First, this collision involved two of what might be called “bodies.” These were the “bodies” of the Spanish as a people and the Inca as a people. The Spanish were most definitely moving at the time. They had come all the way from Spain to what is now Peru for the sake of what some historians refer to as “God, gold, and glory.”
Second, this collision certainly had destructive results. Before the Spanish came, the Inca were lords of a great empire. After the Spanish came, the Inca were thoroughly diminished. Many of them were dead from war or, more importantly, from disease. Their empire was completely subjugated by Spain.
Thus, this can be seen as a collision because the two “bodies” ran into each other with destructive results.