The answer to this question can be found in a dialogue between Young Joseph and an commissioner who had come to organize a new agency for the Nez Perces in the Wallowa Valley. The commissioner asks Joseph why they do not want schools and Joseph says schools will lead to churches. He goes on to say that churches will make the Nez Perces learn to "quarrel about God," which is something he says they never do.
We can interpret this to mean that the Nez Perces did not want to become more Americanized. It hints at the idea that the Nez Perces were content with their own culture as it was. They did not want schools to come in and teach them the ways of the white people, thus making them lose their own ways.