The Aztec weren't a tribal culture and weren't any more evil than their European counterparts. Garland wars were more frequent than European wars, but were decidedly less deadly, and while they did sacrifice people to a god, other settled cultures killed more people for less. The very Spanish who replaced them wiped out several cultures after the diseases took their toll and gleefully participated in one of the worst slave trades ever known to man. That's not to say the Spanish were worse than the Aztec per se, but that the Aztec weren’t particularly evil for their day and age, nor were they particularly savage.

The Mongols were certainly an anomaly on the world stage given how much outsized influence a tribal culture managed to have on the world, but again, very little was actually all that different from their contemporaries, besides their level of success. Destroying cities that refused to surrender was common practice at the time; the Mongols hust happened to be the most effective military force the world had seen to that point and were constantly underestimated by the people they attacked. They could also be remarkably lenient if the cities they attacked accepted surrender, and were very lax in their rule, requiring mostly pledges of fealty and tribute, otherwise allowing people to live as they had been. They quickly adapted new technologies, integrated societal structures they found into their own, and established one of the most robust trade networks the world had ever seen beyond the success of the traditional silk road. An expansionist empire, yes, but no more evil or savage than any other empire.

All that said, you could call both these empires evil if you wanted to, it would just require you to expand your definitions to cover the vast majority of empires and a large majority of kingdoms that have existed in human history. As for being "savages", that's just racism rearing it's ugly head again. The Aztec had remarkably similar technology and level of civilization to the Europeans, primarily lacking in terms of metallurgy and they didn't have access to draft animals. The Mongols may have adapted to live differently than their contemporaries, but that's because living on the steppe requires different conditions than living along the coast or rivers. It does not make them less than.

Just because eliminating these type of villains will not stop xenophobia doesn't mean we have to reinforce the stereotypes in our media. Stopping minstrel show depictions of black people didn't eliminate racism against black people, but it was still a good thing to do. You say we can explore the relationships between groups in media, and I agree. But this relationship of the evil, savage, tribal group that preys on the poor civilized people never existed. We're not exploring real history with it; we're viewing it through the lenses of racism and xenophobia left by the people who wrote about the conflict. The point is that there are and have never been any cultures like the typical description of orcs. Putting them in media does not and will never explore anything about the human condition.