It's important to contextualize this claim. Sally Roesch Wagner is not a scholar of pre-Columbian cultures, but of first-wave feminists, most particularly Matilda Joslyn Gage, and while I haven't read all of her work, the writings of hers that I've seen have been more focused on the idea that this is what Gage and her contemporaries believed. She takes it as something of a given because she is often somewhat credulous regarding the claims in her primary sources - I could list a number of complaints I've had with her remarks on women's clothing in the period, in her writing and in the Matilda Joslyn Gage Foundation's museum - but it's not a claim that Wagner's put forward herself as a conclusion of her studies, if you see what I mean.

Matilda Joslyn Gage (1826-1898) is not a very famous figure today, in comparison to the activists whose names are in the high school history textbooks: Susan B. Anthony, Elizabeth Cady Stanton, Lucretia Mott. For most of the nineteenth century, though, she worked with these women at the head of the movement! Like many of her colleagues, she was raised in an abolitionist family; she also married an abolitionist, Henry Gage, and the two made their home in Fayetteville, NY, available as a stop on the Underground Railroad. While she didn't attend the Seneca Falls Convention of 1848 (which is generally considered the start of the organized women's rights movement in the United States), she did speak at the third National Women's Rights Convention in 1852, when it was held in Syracuse. In the following decades, she would play a large part in the mainstream feminist movement, and even after she broke off from it due to its overwhelming focus on suffrage and its willingness to shelter otherwise conservative suffragists, she continued to passionately advocate for the rights of women and non-white members of American society.

Gage and other feminists from upstate New York were particularly fascinated by the Haudenosaunee (Iroquois), whose culture was leaps and bounds beyond the United States' in terms of women's rights. Lucretia Mott was closely involved with the Seneca Cattaraugus reservation through the Quakers, and unsuccessfully opposed strictures meant to impose Euro-American ideals on female behavior there; she also observed a long debate over the reorganization of their government in which women were accorded as much of a voice as men. In Gage's book, Woman, Church and State: A Historical Account of the Status of Woman Through the Christian Ages: with Reminiscences of the Matriarchate - published in 1893, the same year she was adopted into the Mohawk nation - she noted their tradition of tracking matrilineal descent, their institution of powerful clan mothers and women's councils, and the rights Haudenosaunee women had over property and their children: things that were completely at odds with white American women's experiences. (Overall, this book is a clear forerunner of second-wave feminist histories that uncover vast, peaceful prehistoric matriarchies in Europe and the Near East, and praise pre-contact societies around the world as more equitable than those influenced by Christianity.) Something else she turned to multiple times in the text is how rape and its penalties in a society reflected the status of its women, and it does so in such a way that you're really reminded that this is a primary source reflecting the biases and intentions of its writer, not a secondary source that could be useful as a reference for pre-/non-Christian rights of women. While Gage doesn't claim in that book that pre-Columbian North America never knew sexual assault, other feminist writers of the period would obliquely reference the idea that women in Native American communities were safer when alone with men or walking at night than their counterparts in white towns and cities.

In large part, they were onto something that they didn't have words for in the nineteenth century: rape culture, and the absence of rape culture. "Rape culture" refers to the normalization of sexual assault, and as a result, the expectation that women should be constantly on guard for it and are to blame when not taking enough precautions against it/"inviting" it through behavior or dress. I've written about historical rape culture previously here, in an answer about Outlander, so I won't go into too much detail to explain that rape culture's been a problem in Western society for a long, long time. But an important part of the term is the word "culture". By definition, rape culture isn't biologically inherent, it's societally determined, and it's entirely possible for some societies not to e.g. treat the aftermath of a conflict as a setting for rampant sexual assault. Gage and others were trying to argue that men's and women's inequality stemmed from cultural issues of women's subordination planted deep within Christian, western society.

That's not to say that a society without rape culture would actually be entirely free of sexual assault, but that it would be considered along the same lines as any other physical assault on any other person, rather than something more acceptable and mysteriously impossible to definitively call a crime ("he said, she said"). In the introduction to The Untold Story of The Iroquois Influence On Early Feminists, Wagner describes a conversation that helped her to see Haudenosaunee norms as Gage, Stanton, Mott, and others did:

About eight years ago, early in my new phase of research, I sat in the kitchen of Alice Papineau-Dewasenta, an Onondaga clan mother. Over iced tea, Alice described to me the unbroken custom by which traditional Iroquois (Haudenosaunee) clan mothers nominate the male chiefs who go on to represent their clans in the Grand Council. She listed the qualifications: "First, they cannot have committed a theft. Second, they cannot have committed a murder. Third, they cannot have sexually assaulted a woman."

There goes Congress! I thought to myself. Then a wishful fantasy occurred: What if only women in the United States chose governmental representatives and, like Haudenosaunee women, alone had the right "to knock the horns off the head," as Stanton marveled -- to oust officials if they failed to represent the needs of the people unto the seventh generation?

And on the flipside, a lack of rape culture also means that sexual assault wouldn't be seen as the primary weapon against women in rival or enemy social groups or a way to humiliate said groups. Firsthand accounts of women's abductions by Haudenosaunee and Algonquian men in the seventeenth and eighteenth centuries reported no rape, despite continual fears of it by white settler-invaders, and despite the amount of sexual assault that was and would be perpetrated by white men against women of most if not all Native American cultures. There are always questions of bias and omission in primary sources - women could have feared ostracization for having been sexually assaulted by non-white men - but it's telling that they largely all agree in this way. Some accounts of the period do mention it as part of the treatment received by young women who were not integrated into any Haudenosaunee or Algonquian families (as most captives were "adopted" as either low-level family members or servants), but it was very far from the norm.

Many have made the mistake of taking this localized absence of rape culture in the northeast to be indicative of the entire continent or as a total ignorance of sexual assault, largely as a result of buying into stereotypes of Native Americans as "noble savages" who were and are uniformly and supernaturally kind and in touch with nature. Accounts from farther west showed that members of some Plains cultures, for instance, did regard sexual assault as a suitable weapon. But the claim that Wagner has amplified is specific to the northeastern corner of the United States.