I don't think "well the game has magic so it's ok to discard any inconsistencies in plot, world building or historical accuracy" is a good argument. Instead, simply say that it's a relatively minor change that doesn't have that much impact. After all I'm sure there's other historical changes made throughout the franchise other than things required by the plot .
Heck, it would prove that people complaining are doing so because of racism even more since they're not complaining about those changes.
Historians don’t make a lot of strong claims about Yasuke - there’s very little written on him (in English, that I can access through journal databases) other than a pop history book that seems to play a little fast and loose with the facts.
I think the lack of information makes him a better protagonist though.