While we shouldn't deify Lincoln or any other person as such, it was a military tribunal that condemned 303 participants in the Dakota Uprising of 1862 for murder & rape. Lincoln carefully reviewed the cases & commuted all but 39. Later, Gen Silbey telegraphed that he had doubts as to the guilt of another, so Lincoln commuted his sentence as well.

He allowed 38 executions to take place. Indeed the largest mass execution in US history. But Lincoln took care to distinguish between those who participated in rapes & massacres vs. those who merely fought.

I think Lincoln's fault lays not in the executions but the conditions that led up to the Dakota War. His BIA agents were so corrupt that Santee Sioux, led by Little Crow, were left starving, their children had nothing to each because agents stole supplies & withheld funds the Sioux were promised in exchange for coming into the reservation.

On their side, they had very little choice. Rebel or starve. But settlers, officials, women & children were massacred. It was a bloody, awful conflict. There were no good guys. But Lincoln certainly has to take the blame for presiding over such a corrupt & inefficient BIA.