The government did move away from forced separation, but not right away. After all, the Indian Wars of this time were focused on forcing the Native Americans onto reservations. However, toward the end of the period, the government did try to make the Indians more like white Americans through such things as the residential boarding school program. We must note, though, that this did not really make for integration into American society. The government was trying to destroy Indian culture, but it was not doing anything to actually integrate them into white culture.
In the 30 years after the Civil War, although government policy towards Native Americans intended to shift from forced separation to integration into American society, attempts to "Americanize" Indians only hastened the death of their culture and presence in the America. The intent in the policy, after the end of aggression, was to integrate Native Americans into American society. Many attempts at this were made, ranging from offering citizenship to granting lands to Indians. All of these attempts were in vain, however, because the result of this policies is much the same as would be the result of continued aggression.
Beginning in the 1860s and lasting until the late 1780s, government policy towards Native Americans was aggressive and expressed zero tolerance for their presence in the West. In the last 1850s, tribal leaders and Americans were briefly able to compromise on living situations and land arrangements. Noncompliance by Americans, however, resumed conflict. The beginning of what would be called the "Indian Wars" started in Minnesota in 1862. Sioux, angered by the loss of much of their land, killed 5 white Americans. What resulted was over 1,000 deaths, of white and Native Americans.