That is an important distinction: the megacorps are not evil as such, just in it for the money. Even the "most evil" megacorp, Aztechnology, generally uses the nasty stuff like blood magic as a means towards greater profit rather than any grand plans for world domination. And on the flipside you have the megacorps many people consider "better" than most still dabbling in horrible, horrible things. (Like Ares with their experiments on insect spirits or NeoNet vivisecting technomancers... even Horizon has had their morally questionable brainwashing programs discussed.) Really, it seems like Evo is the only AAA that hasn't committed any horrible deeds that I remember.
But again, I have to say I'll be disappointed if it turns out that Horizon has some ::cue scary music:: dark secret behind it. The Universal Brotherhood was like The Sixth Sense of Shadowrun... it was powerful because it was the first big, dark twist. Currently Shadowrun is in danger of being like M. Night Shamalamadingdong, churning out "twists" like an assembly line. Honestly, if the developers want to shock Shadowrun fans, it will turn out that Horizon is an actual socially-responsible megacorp.