Lincoln wanted to set an example. He didn't want to contend with a Civil War and an Indian uprising simultaneously. It worked.
Uh, the sad truth, they were hanged for participating in an uprising, against an invading enemy.
The Indians never fought the White man except, on their own soil, in their own country, only then did they resist the invader, the United States was that invader.
Lincoln sanctioned the ongoing genocide of nations, tribes and people, in short, men, women and children were robbed, starved and slaughtered, all under the auspices of the stars and stripes.