Treatment of Native Americans

This is an uncharacteristic post, but I've been thinking lately about the expulsion of the native americans. My idea has always kind of been that when you lose a war the consequence is that you have to do what the conqueror says. I've been rethinking that in a few ways.

First, if the war is not morally justified, then acts based on victory in that war cannot be morally justified.

Second, while conquest may come with various perogatives, the conqueror retains the power to waive those perogatives by contract/treaty; where that is done, the perogatives should be considered waived.

Third, and I'd love to look into this more because I know nothing about it, a war between nations determines the sovereign of the land, that is, which government controls it; it does not necessarily eliminate private property held by newly acquired citizens. I'd be very curious to know how we treated settlers in what was once Mexico after the Mexican-American War took land. My guess is that the sovereignty transferred to the United States, but the residents didn't lose all rights to their private real property.