The characters all have tan skin, meaning they're supposed to be Indians, not white folks playing Indian. The art, architecture, writing, calendar, and numerical references (baktun) are reasonably accurate, especially for a cartoon.
With a few exceptions, the characters' appearances are good too. But Marge is wearing some sort of slinky savage-girl costume. A few of the others have too much skin showing. The working classes may have gone half-naked in the heat, but I think the elite mostly covered themselves.
Moe, Chief Wiggum, and the other officials have masks painted over their eyes. This kind of look seems more like a movie fiction than a reality. It serves to make the officials seem scary.
For starters, the Aztecs were the ones known for human sacrifice, not the Maya. Human sacrifice was relative rare among the Maya, so focusing on this makes their civilization seem more barbaric than it was.
Though Mayor Quimby says a prisoner is to be sacrificed to appease the gods, this is a gross simplification of the complex Maya religion. As Wikipedia explains:
Sacrifice in Maya culture
Using a clever Maya slide-rule, Professor Frink calculates that the calendar will end in 2012. We flash-forward to the present where three Maya gods smash everything.
First, I'm not sure the Maya gods even exist in human form. My impression is that they're more like forces that take on aspects of humans or animals. In other words, amorphous shapeshifters, not beings with a standard appearance like Zeus or Odin.
More important, no one has claimed the Maya or their gods would themselves cause the "prophesied" destruction. The Maya supposedly predicted the end, but it's not as if they wanted it to happen. They're the messengers, not the instigators. If the world were to end in 2012, it would happen via a natural cataclysm, not a godly temper tantrum.
Finally, as I've noted before, the world's ending in 2012 is a myth:
Maya mural contradicts "doomsday" myth
World won't end in 2012?
The calendar rollover signifies, at most, a symbolic turning point in history. If anything did happen, it would be a process of change and renewal, not destruction. For instance, if people started to care about climate change, it would "destroy" the old mindset of greed and selfishness.
So the Simpsons' scenario is doubly wrong. It implies the Maya expect the world to end and, worse, are causing it to end. Neither claim is true.
This destruction conveys the same idea as past centuries of stereotypes: that Indians are savage barbarians with no regard for life. That they exist primarily to crush, kill, and destroy things. That despite their art and architecture, they're little more than animals in human guise.
That's stereotypical if not racist. Many Maya Indians would disagree with this characterization of their ancestors. They're alive and well and some of them probably watch The Simpsons.
The Maya sequence gets points for starting off with a decent depiction of the culture. It loses those points and more for presenting a human sacrifice. And worse, for fabricating the meaning of the calendar's end. For portraying the Maya deities as cruel and inhuman enough to destroy life on earth. The Old Testament God may be a genocidal maniac (see the Flood), but Native gods aren't.
For more on The Simpsons, see Navajo Boy in Brother's Little Helper and "Arapaho Ghost Dancer" in The Simpsons.