The New Conquest Historians are a loose group of historians studying the early Spanish conquest. Some of the best known writers in this group include Matthew Restall, Camilla Townsend, and Kris Lane, among others. One of the main focuses of these researchers is to emphasize Indigenous agency in the face of colonization - how Indigenous people and nations formed alliances with colonial powers, resisted them, or generally adapted to colonialism. The point of this according to these historians is to emphasize that Indigenous people were not helpless victims in the face of European conquest, but powerful historical agents in their own right.
While this is a laudable goal, I was wondering if it might unintentionally provide ammunition to colonial apologists who want to deny the atrocities of colonialism. Might some bad faith commentators use the complex relationships between Indigenous people and colonial powers to say that “actually colonialism wasn’t that bad”, or “indigenous people brought their oppression on themselves”, among other genocide-denial tactics? I was wondering what AskHistorians thinks.
I've held off answering because the Americas are wildly out of my field (which is early Christianity), but since it's been several days with no sticking responses, I'll address the theoretical aspect of your question and perhaps the mods will have mercy.
New Conquest History has a lot of similarities to (and probably branches out of, at least in part) postcolonialism, which was originally developed in the context of former British colonies, especially India. A couple of major early writers were Edward Said and Homi Bhabha, both of whom challenged essentializing language that divide human cultures into stereotypeable groups (e.g., "Eastern" and "Western," or "First World" and "Third World"). Similar to NCH, the idea is that such language removes agency from all actors but especially from subalterns, and can promote essentialist narratives like the idea that European colonizers naturally and easily subjugated the peoples they colonized.
There are naturally going to be some differences between societies that are no longer (directly) colonized, like India, and places like the Americas, but I think the basic structure of the theory holds. The main feature of postcolonialism, as I read it, is the idea that subaltern people possess agency before, during, and after colonization. That doesn't mean that they "allow" colonization to happen, in the victim-blaming sense that you're worried about, but rather that individuals and groups have available a variety of responses to colonialism that range from full cooperation/assimilation to full and violent resistance, and usually fall somewhere in between. One common response in both colonized and postcolonized societies is mimicry, whereby the colonized adopt and adapt modes of the colonizer. An obvious example is the proliferation of European clothing styles throughout the world. Importantly, postcolonialism acknowledges that people and societies who engage in mimicry do it for their own reasons, which may or may not have anything to do with the colonizer's reasons, and may or may not align with the reasons of others engaging in similar mimicry.
To get to the meat of your question, in my opinion postcolonialism and similar approaches actually help diminish the possibility for bad-faith arguments like the ones you suggest. First of all, remember that those arguments already exist, and are major tent poles in pro-colonialist arguments. See, they all wear our clothes/speak our language/follow our religion: that means they know we're right/superior. Postcolonialism destabilizes those arguments by returning agency to colonized people and acknowledging a range of possible responses to oppression and possible reasons for each response. Yes, they wear our clothes, but they do so merely as a means to survival, or in ways that preserve their own cultural logic and not ours, or as a means of subtle mockery. Yes, Christianity has globalized, but Christianity in Nigeria looks very different from England or Korea or Mexico. Postcolonialism lets you dig into those differences and recognize them as agency without diminishing the reality of domination.
If you haven't read it, I highly suggest James Scott's Domination and the Arts of Resistance. It's sort of a classic text by now and as such can certainly be added to and further complicated, but it lays some fantastic groundwork for understanding the variety of ways that colonized and otherwise subjugated people can perform resistance without or before engaging in outright violence. I'm not exaggerating when I say that it changed my entire approach to my field.