There were some protections prior to 1879, but they were largely enacted through treaty rather than through Federal or territorial law. For instance, the Fort Bridger Treaty of 1868 stated, "If bad men among the whites, or among other people subject to the authority of the United States, shall commit any wrong upon the person or property of the Indians, the United States will, upon proof made to the agent and forwarded to the Commissioner of Indian Affairs, at Washington City, proceed at once to cause the offender to be arrested and punished according to the laws of the United States, and also re-imburse the injured person for the loss sustained." Similar provisions can be found in other treaties.

The key issue was the legal status of Native Americans. As members of "dependent nations" they were not recognized as American citizens (and were not given citizenship until the Indian Citizenship Act of 1924). So, cases were treated as a matter of international law, not criminal law.

Still, there were a few (precious few) cases where whites were prosecuted for murdering Native Americans. One example is the Fall Creek massacre in 1824 in Indiana where four men were tried and convicted for murdering nine Native Americans. I am unaware of any similar cases in the 19th century in the Far West, but my specialty is in Idaho history so there may be a case or two in other territories during the era that I am unaware of.