You can also find some examples from the U.S. interventions in the Caribbean during the inter-war period. Haiti springs most quickly to mind, but there are others.
Dealing with the Indian Wars, there are a number of factors that come into play. Chivington was never held to account for a number of reasons, one of which was his status as an officer of volunteers (putting him beyond the reach of military justice). That was actually one of the arguments against using those troops on the frontier (made before the Civil War, so it wasn't a result of post-War second thoughts). The Marias River massacre in 1870 was another example...one that effectively destroyed the plan to shift control of the reservations to the Army and led to Grant's "Peace Policy." Major Baker, commander of the forces that attacked a Piegan band camped near the river, was a known drunkard but was never charged. There is also the strong possibility that the camp he attacked was intentionally misidentified as hostile by a scout who had connections to the band Baker was supposed to be hunting. A final example is the Camp Grant Massacre, carried out by both natives and citizens in 1871 near Tucson, AZ. No real charges resulted from Camp Grant, even though it sparked a major Indian war in the area. Territorial politics played a role, of course, but it should also stand as a stain on George Crook (often proclaimed as the Indian's one true friend) that he did nothing to bring the perpetrators of the attack to justice and instead worked indirectly with them to discredit the officer (a Lieutenant Whitman) who had established the camp and was trying desperately to keep the peace in the area.
The attitudes of Army officers towards the Indians is a fairly complex question, and varies greatly depending on which officer you're considering. Some were realistic enough to understand what was happening, some hated the Indians, others were indifferent. Many blamed the Indian Bureau and local civilians for Indian troubles. I don't know that there was one overall "view" held by Army officers of their opponents.
An interesting point of comparison might come from looking at the conduct of volunteer forces in places like Eastern Kentucky or the Kansas-Missouri border region during the Civil War. Clearly peer-on-peer, and at times kin-on-kin, but the fighting there was often far more ruthless than that encountered on the plains. Some of the Indian conflicts (such as the Army's prolonged pursuit of the Nez Perce in 1877) were almost conventional affairs, and certainly more "civilized" than what went on in western Missouri and parts of Eastern Kansas during the Civil War and before.
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