They create the drugs in the Mojave, sure.
They're the suppliers of the fiends, who're one of the biggest (and most brutal) raider gangs in the wasteland.
And they raided some NCR caravans before Bitter Springs.
I'd argue that raiding caravans as opposed to buying from them is rather evil.

But remember that NCR wanted them dead in FO1 and FO2 as well.
...There was a pretty good reason to want them dead in FO1, what with how they kidnapped Tandi in hopes of getting Aradesh to surrender the town. They also kept slaves - remember how the leader had two slave girls you could rescue, and who thanked you profusely for liberating them?
The Khans weren't nice people in FO1. In FO2 they lie to the people of the squat in order to use them as human shields against the NCR's military, so they weren't nice people there either. Also remember that they're raiders. Not peaceful farmers or artisans or anything. They make their living off raiding, stealing, killing, and looting.
Their initiation rites are also excessively brutal.
Really, it felt good to gun them all down. Though perhaps that was the fact that they'd apparently escaped my vengeance twice before even though I
thought I'd cleansed the wasteland of their filth back in California. Twice.