There's no objective rubric by which to compare or call one side definitively wrong. It's just your opinion that one side was "better" than the other.
That we haven't found an objective rubric doesn't mean one doesn't exist. Objective science has always existed in its entirety, we just figure out more about it as we go.
Let's say you're sitting next to Hitler staring at a 1-way glass wall that looks into a concentration camp's death chamber. You see about 50 emaciated, bald and naked women and children walk in and he explains to you that they think they are about to be be showered, but they are really about to be given zyclon B gas and killed. Sure enough, you watch in horror as this begins to happen and you watch these people die over the course of several minutes, many of them running around, screaming, choking, in agony, etc. It is a truly gruesome sight. Soon there are just a few twitches from the pile of corpses on the floor.
What do you do? Do you calmly look over at Hitler and say, "wow, I am not used to a sight like this because my culture is so different, but I really have a lot of respect for how you guys do things over here." But thinking then of the families and loved ones who were just torn apart, you ask, "are you sure you really have to kill people like this though?"
He replies, "hey, it's all just an opinion, remember. We are just the same as you, that is, without moral value whatsoever because it's all relative. Who would you be to say we are wrong for doing this? That would be your opinion."
*
And I'm not
just trying to appeal to emotion here, but I think that story is important. There are possible rubrics that transcend culture, government, and religion. People's well-being can be measured many ways, just like their physical health can be measured many ways. There are actions that serve to increase the well-being of individuals, the community, and the world, and there are actions that make people suffer. The axiomatic foundation of objective morality is that suffering is bad and well-being is good. Those things can be measured.
The early 20th century US example of sterilizing low IQ folk actually informed part of Hitler's eugenics program.
If you're saying that Hitler and them really thought it was the best course of action based on the accepted beliefs of the time, that doesn't make it any more right. Wrong is wrong, whether or not you know you're doing it.