First, at Genghis Khan's time, in the 13th century, it was accepted that an army could massacre the population of a city that resisted thehm. It was something accepted, not the exception. For example, let's see how the good Christian Europeans massacred the citizens of Jerusalme in the First Crusade:
I really doubt that proves it was accepted. The massacre of Jerusalem is one of the incidents known for it's bloodiness, it's known because it was an exceptional incident.
Secondly, even if it was accepted, it's at best an excuse you can allow to Genghis Khan.
Also, there is something you seem not to understand. Historians have to judge events by their effects, not by their morality. The conquests of Genghis Khan were brutal. But their effects were mostly good:
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So, Genghis Khan's influence was more good than bad. So, he is Great. And this is not based on moral standars (which should not affect a historian), but on his influence on the world. Which was mostly good.
Wouldn't it be more correct to say that historian's job is not to evaluate on scale great - non great, but on influential - non influential.
Also, I don't think you're omitting moral consideration above. Already that you speak of "the good" G.K. did suggests it. Your just omitting a part of it, namely killing people. In essence you're saying that reviving trade, unifying China etc. weight more than the human lives he ended.