People thought differently, it was believed that bringing civilization was their duty a social responsibility, resistance to assimilation was a rejection of civil society and indicative of a "savage" nature than needed to be tamed or brought to heel. Tearing kids away from their families and putting them into regulated western schools( with religion) was considered a good way of breaking this "behavior". Eugenics, phrenology, racial based discrimination, etc. was all considered acceptable at different points in the relevant history related to these events.