The Emperor's New Groove is just one of those films where you look at all the historical inaccuracies and go "heh, that's funny".
What, you think 15th century Inca had roadside diners that served giant pillbugs? You think it had waterslides? You think it had rollercoasters? You think it had spinach puffs?
All that said, they did get some things right- like the importance of llamas, and the lack of pants. Like... in what other movie would you see every single man wearing a skirt or dress, even when it takes place in ancient times in a region without horses?
Also, both Kuzko and Pacha have aquiline noses, a feature that is almost never depicted in fiction outside of villains. And yet Kronk, who is a villain for most of the movie, doesn't have it, and neither does Yzma.
Kronk is Jewish. He comes from a community of Jewish people who all live in 15th century pacific South America. He also lives in a world where 15h century pacific South America had things like rollercoasters and spinach. It's a comedy full of historical inaccuracies- if the only thing that bothers you about it is Kronk being Jewish, you're not a history buff, you're antisemitic.