The parallels to the European genocide of Native Americans has significant consequences to two groups of people. The first is the white supremacists/edgelords who think an invasion from thousands of years ago means the actions of colonial Europeans as well as ongoing social justice issues with native Americans/reservations are somehow justified or deserved. The second is the far larger but far less dangerous group of people who think native Americans are somehow inherently morally superior and/or that European colonialism is responsible for all the world's problems. To them it's an article of faith that aboriginal peoples do not and cannot commit large-scale atrocities.
These two groups can make discussing and teaching American pre-history very difficult.
1. pre-Clovis people were so thinly spread that Clovis was able to just fill in the gaps
2. pre-Clovis people had actually essentially become extinct before Clovis arrived. It's not easy to see how that would be the case in a continent(s) of this size, but not actually implausible.
3. as a combination of the two, pre-Clovis culture was completely nomadic, and their constant migration kept them out of the way of Clovis until a point where their population was so diminished as to leave no descendants, even via inter-breeding.
But hints that there were people here before that have been around for a long time, starting with the Monte Verde work in Chile a few decades back.
And I don't recall any particular "mess" from indigenous americans.
I mean, scientifically there's definitely a big question of why the population density of the earlier settlers seems to have been so low (vs. clovis, which basically exploded onto the scene and went everywhere on the continent very fast), or why they are not identifiable in contemporary DNA (which very closely supports the "clovis only" hypothesis).
But there's no politics at work here. Stop it.