It can be problematic to view historical events through a modern day lens; to apply modern ethics to past events. Genocide was a term coined in 1944, for instance.
So if we are to judge those by the ethics of their own time. Battle of the Little Big Horn was
1876.
The first Geneva convention was 1864 and prior to that there were various treaties governing rules of war.
The continental army from inception had a code and rules of conduct.
The
Lieber Code was issued as General Order No. 100 in
1863. Signed by Lincoln it dictated how US soldiers should conduct themselves.
Article 44:
"All wanton violence committed against persons in the invaded country, all destruction of property not commanded by the authorized officer, all robbery, all pillage or sacking, even after taking a place by main force, all rape, wounding, maiming, or killing of such inhabitants, are prohibited under the penalty of death, or such other severe punishment as may seem adequate for the gravity of the offense.
A soldier, officer or private, in the act of committing such violence, and disobeying a superior ordering him to abstain from it, may be lawfully killed on the spot by such superior."
I don't really think it's up for debate that soldiers on the us frontier including Custer and his men committed court martial-able offenses based entirely on the laws of their era.
Native American's certainly used similar tactics on settlers, eg. Comanche in Texas, though they were not bound by their own law nor any treaties. Ethically I don't think there is a difference and I am not giving the total war tactics employed by various tribes a pass, but I think we do have to acknowledge that a sovereign nation following it's own rules is different than Custer disobeying US military code.
Lastly, the Lieber code has been used as a blue print to inform modern rules of war. It's how we got the Nuremberg Trials and the trial of Calley et. al for My Lai.
US and international law has dictated for almost 100 years that "just following orders" is absolutely not a justifiable defense. Solider's have an obligation to disobey orders that are palpably illegal, so clearly illegal that any reasonable person would have known it was illegal. I doubt very much anyone now or in 1876 would disagree that rape and murder of unarmed women and children is "palpably illegal".