What are some historical real world examples of a objectively good end justifying a terrible means? For "historical," we should probably look back to pre-WWII history.
Bullgrit
At the battle of the bulge in WW2, the americans had to machine gun to death the german prisoners so they could move on and continue fighting to overthrow the nazis and win the war. This was clearly a violation of the geneva convention, but it had to be done, there weren't soldiers that could be spared to guard the prisoners.
Anytime there is war, there is going to be "incidents" that are terrible and awful, the fact that most civilians don't know or want to know about them is fine. If the war is fought to prevent tyranny like WW2, then I think you can say those things are probably ok in the grand scheme of things. I just feel bad for the line soldiers that have to do the "evil" and then live with what they did for the rest of their lives.