"Kill everyone who isn't us" Is pretty damned evil as a motivation. even if it doesn't specifically include a couple of minor factions. But again, everyone in Kenshi sucks, to some degree or another. Most of them don't hate you for not looking like them or having the ability to conceive a child tho', making them markedly better as people than the Okranites.
Yes, the Shek are racist assholes who just want to fight and die in glorious battle, they aren't exactly functional as a society either. And the U.C. are capitalist aristocracy to an actually insane degree, making them even more unpalatable than the Shek to me personally. And pretty much everyone else wants to steal from you, kill you, or for you to leave them the hell alone.
Hell, the player faction can be even worse depending on the motivation, I have actively fed prisoners to fogmen in a couple of my more RP directed saves, just because that's what the people involved would do to their enemies.
All the major factions are demonstrably negative, and the degree to which the player perceives them as such will depend entirely on their internal biases, so for myself and others with similar biases, the religious, murdering, misogynistic psychopaths are the worst faction. To others, who view conflict, elitism, wealth disparity, classism, or other factors as larger detractors the other factions will seem worse.
Edit: As an addendum, I don't even 'hate' the HN, I just find them the least tolerable overall.