Very good question, and rather tricky to answer, because I do agree with a couple of things she says. But I disagree (like you) with what seems to be her blanket conclusion: that the form of ‘Christianity’ that influenced the settlers to annihilate the Native Americans is true Christianity.
There are many ‘types’ of Christianity, as she mentions, and, given how you read the Bible and interpret it, people can and do come to different conclusions. I would say that the same ‘Christianity’ that was quiet in the face of the waging of war on indigenous peoples was the same ‘Christianity’ that justified and morally propped up the trans-Atlantic slave trade and Jim Crow laws.
This, to me, is an unanswerable question. We cannot answer for definite for other people, esp. when those other people live miles removed from us in time and culture. We can look at societal trends, which is what she does as a sociologist, but, from there, it’s (educated) guesswork.
It’s my guess that this type of ‘Christianity’ – the one that can morally justify violence by certain people on another group of people or person – was, indeed, a ‘majority’ Christianity at that time in many ways, so that even if a minority were the ones actively annihilating the Native Americans, the majority weren’t that concerned. Though I would like to think that another minority was actually concerned, sadly, I can’t think of any off the top of my head. (The Quakers??)
What one really need to look at is the theology of this majority ‘Christianity’ of that time and place and ask, how did they justify these actions? How were they interpreting the Bible and how did they draw these conclusions that led to these actions? It probably won’t take long for you to find some premises you disagree with and to be able to offer how you interpret things differently.
As a P.S. I’d like to add that it’s easy to not challenge those who are committing violence against human beings when one believes that the victims are not fully human.