Well, when you think about it, Hojo created Sephiroth, President Shinra only cared about controlling the world and just killing anyone who even accidently find out and didn't want anyone to get in the way, not to mention that Hojo never told Sephiroth about Lucrecia, because that idiotic senile evil bastard wanted to prove his theory on Jenova, and when Sephiroth disappeared, that kinda back-fired, so he decided to use Cloud, Zack and eleven other people as vessels and clones...
Warning: SPOILERS-Kinda like what Xehanort's done in KH DDD.
Besides, it wasn't Sephiroth's fault. First he thought he figured out the truth, then turned to blame humanity, then slowly became under control of Jenova before he managed to use her powers but was far too late to be saved, because Hojo was extremely close in getting what he wanted, because as far as Hojo's concerned, the entire Planet and all things and people living in it are nothing but things, objects and subjects for him to experiment with because he thinks he's the only human being ever.
In the end, Sephiroth was a victum himself, even before his birth.
Zack had go through fights against Angeal, Genesis and Sephiroth, and Sephiroth is the only one Zack was unable to defeat, but was at least able to protect Cloud after escaping the ShinRa Manor right to his death outside of Midgar. Cloud was innocent and didn't know until Nibelhiem and that he was rendered into Mako poisoning no thanks to Hojo until things got out of hand just before the beginning of the original game.
As a result, Hojo was just too evil to be considered human. At least Gast didn't have any intentions in experimenting on his own wife and child and even tried to protect them.
President ShinRa just wanted to have super-human warriors and make everyone else his slaves by putting up lies. I can cope with Rufus because he's not as crazy and has learned some lessons after the original game. I think Rufus's intentions was to prevent history from repeating itself by killing off scientests who plan on bad experiements and even wanted to hide(and probably later destroy) the remains of Jenova's head to prevent another calamity.