How were white people dealing with Native Americans at the end of the Indian wars as opposed to at the beginning, as told in Bury my Heart at Wounded Knee?

Bury my Heart at Wounded Knee by Dee Brown starts off by looking at the Indian wars of the East that took place before 1850.  Many of those looked like open wars of extermination and subjugation.  He also talks about Andrew Jackson's Indian policy of creating an Indian territory.  The army was in charge of protecting white rights above native rights.  Contrast this with the end of the book, the Wounded Knee Massacre.  The governmental bureaucracy took a more active role with the Department of Indian Affairs.  There was no an attempt to "pacify" the natives and drive them onto the reservations by destroying their way of life, mainly the pursuit of the buffalo across the open plains.  The goal was to assimilate the natives the best way the government knew how--to turn them into farmers.  It was only when the natives started acting in non-white ways on the Pine Ridge and Rosebud Reservations with the Ghost Dance did the massacre take place.  To Brown, the attitude of whites turned from conqueror of the wilderness to a more paternalistic, high-handed view that they alone knew what was best for the Native Americans.