I'm not going to dismiss the Spanish conquests, but I will say that if you're going to be making alt-history, dismissing the events because of the means is a much better idea than dismissing the means because of the events.
Understanding why or how something happened helps you immensely in determining what would make likely and plausible alt-history, knowing what happened means you know the Original Timeline, but helps jack squat in alt-history.
That's a fair and reasonable point, and I can't disagree with it, particularly in a game design / alt. history sort of way. To that point, it'd actually be cool if you could conquer the New World in the same way that Cortez and Pizarro did - very quickly thanks largely to luck and disease.
But unfortunately you can't.