Did you read up on the lore regarding Nipton? As Vulpes pointed out it was a pretty eff'd up place filled with all kinds of bastards. And in a time of war it did serve as the perfect place for the Legion to make its mark.
The mayor may have deserved the cross but what about everyone else who lived there?
The people of Nelson? It was an NCR camp before the Legion took over so that's a moot point.
It was a settlement it had civilians who were slaughtered.
The Legion's treatment of women? Women do have their place in the Legion, but the military is not one of them. Keep in mind that all you see from the Legion in this game is their war camps and they gotta do something with their female captives.
Women are treated as slaves and breeding stock period. When they integrate a tribe the sick and elderly are killed, the women sold as wives. Does that sound like the behavior of a group its safe to live under? There is no word no mention of the Legion treating women as anything more then property by any NPC with the exception of the Courier[if female]
Women aren't allowed to run a caravan company in there territory according to Cass. And why do you think Gloria Van Graff who hates the NCR double crosses the legion by luring them into an NCR ambush? Because she's a woman and knows the NCR will let her do business but the legion treats women as property.