The politics behind combating Afrocentric theories that rob indigenous Americans of credit and agency are indeed complex. I've written a bit here in critique of a popular author who suggests we teach trans-Atlantic contact theories because they "provide a fascinating story." It's a noble goal, of course, but it comes with a secondary message: it's okay to propagate histories with what you yourself admit to have "low" evidence... if it has a nice purpose.

On the other hand, archaeologists generally attempt to work with or alongside indigenous origin stories and oral histories (or at least we're trying to more). You can find some great discussion on "Apparent Contradictions" in indigenous sources from /u/snapshot52 here, with some additional sources from myself and /u/drpeppero.

What's the difference?

Indigenous knowledge does not present itself as archaeology or history. It operates under its own epistemology. Psuedohistory's proponents present themselves as academics operating with the same level of scholarly inquiry, self-critical analysis, and transparent methodology that characterizes archaeology. Theories like pre-Columbian African contact only pretend to such a status; they are of course based on a distorting obsession with singular bits of "evidence" that ignores entire fields of research.

Thus, the term "psuedohistory" for Native American knowledge isn't appropriate. It both negates its value and overlooks the concerns of historians about the popularization of pseudo theories.

How do we combat psuedohistory?

The best is to teach good historical practice. Teaching history as facts and stories only encourages the common psuedohistory assumption that there is some "official history" that academics write; anything that's not in it is heresy. Contradicting stories are thus "edgy" or "brave." The main appeal of psuedohistory is its anti-establishment sentiment. But in academic history and archaeology, contradictory interpretations are our lifeblood. If everybody agreed and new data didn't change our interpretations, we'd have nowhere to go. I'd be wasting my life on a PhD so much more than I already am. There have been literal bar fights over archaeological theory. Exposing students and the public to that process is essential and must begin early in schooling.

This is also how we should approach psuedohistory that emerges out of legitimate anti-establishment grievances. Academia has slighted Africa in general, and it is not the content of Afrocentricist pseudoarchaeology that makes it bunk. It is the manner in which it attempts to legitimize its knowledge. It fails the tests of the very epistemology it claims. This is where we must focus our critique, and it can only be effective when there's a general understanding of what good historical knowledge-making is.

Furthermore, even though most any religious tradition does not align with historical or archaeological knowledge, there are theologically sound and theologically unsound claims within each religion's epistemology. Good theology and good history are both important, yet neither good nor bad history is going to have much say in the spiritual epistemology. When we're evaluating claims that originate in different epistemologies, it's absolutely necessary that we do so within the theoretical realm assumed by the claim. Being comfortable that different interpretations from different approaches is not inherently contradictory is crucial to any holistic historical understanding. This is quire thoroughly addressed in the linked discussion on indigenous sources.