There don't have to be just two possibilities to explain what happened. And more than one explanation can be true.
A quick and imperfect summation of European culture's relevant features at the time America was "discovered" and settled: Landowning most places was limited to the aristocracy. Most people weren't allowed to own land, only rent it from the local lord; rent was the source of most of their wealth. The continent was periodically rent with wars, some of them because of religion. The average person had no control over much of anything. Merchants were increasing in numbers and were asserting themselves as something of another force to be dealt with in terms of having wealth and aspiring to power.
Add the discovery of a new continent, limiting ourselves just to land now the United States and Canada, and the first thing that happened was creation of land grants by European royalty to some aristocratic supporters as a way of expanding their wealth. The early settlements were not all just people fleeing religious oppression, they were speculative schemes organized by entrepreneurial interests, both royal and merchant-sponsored, to create new towns and new farmsteads from which rents and trade could be obtained. Some of these efforts were "state sponsored," ie., national (royal) backed. Others were backed by consortiums of merchants who pooled their money, funded creation of a town in the new world, and hoped for a return on their investment. You can still take land in, say, New Jersey, and trace the deeds back through time until you get to the original land grants from the king to two individuals. And in the late 1600s and early 1700s, there was debate and unrest here about the abolition of the kind of rent system that dominated England and Scotland. To this day county government in New Jersey is known as the "board of chosen freeholders," ie, people who actually owned land picked just by others who owned land to administer counties and do things like improve roads and build bridges. The system of picking them changed, of course, but the title lingers as a kind of historical artifact.
Consider the culture upon which this descended: While there were recognized areas that might be considered "Lenape land" rather than "Mohawk land," the idea of a specific, identifiable piece of ground being owned by an individual, whether a chieftain or a rank-and-file guy, wasn't in the paradigm. No culture is monolithic, though, so when some chieftains were asked to trade their land for various goods that very much offered an improvement in their life, they went ahead and did it. That the Europeans then, in effect, fenced it off and started farming, creating resentment among all the indigenous people affected by the actions of some of their number.
The degree to which indigenous people were then either deliberately or accidentally eliminated varied from place to place, with the English at one point actually recognizing one coalition of tribes as a sovereign nation just like England.
It was, given the paradigm from which it sprang, inevitable that the pressure from Europeans to own land would be unstoppable. It was a privilege to own land, and a sign of prestige and a ticket to power. And there were millions upon millions of acres here, a huge magnet. Again, no monolith: People who thought nothing of deliberately giving blankets contaminated by smallpox victims to Native Americans came over along with others to whom that idea was barbaric.
The trick to perhaps presenting a premise to your history professor, whatever you choose, might simply be to avoid the mistake of attributing deliberate, articulated motive to what really was the outcome of contact between two mutually exclusive cultures. Even had there been no creeps willing to use genocide, even if there had been no deliberate efforts to wipe out the buffalo to destroy the Plains Indians "commissary," their way of life depended on communal "ownership" of vast tracts needed for hunting and agriculture and the European model was fueled by a burning quest for land divided up and controlled by individuals. Since the European was, relatively speaking, more technologically advanced and more powerful, it inevitably survived and dominated.
People always seem ready to assign evil motives to the Europeans, on the argument, apparently, that because the Native American culture was destroyed, destroying that culture was the reason Europeans came here. Stated like that, it's obviously nonsense.
Part of the problem you're having is that you intuitively know that, but explaining it as a "counter argument" requires you to take it seriously or, put it another way, you have to accept a "judging" premise and have no idea how to "counterjudge" it because you're a perceptive, not a judger. I'd just go with some observations on culture clash.
Be glad you have such professors. When I was in school it was all just information and facts and it was boring beyond belief.
