But yeah Sephiroth wasn't controlled by Jenova though learning about her/having her alien genes certainly ended up not being good for anyone.
Well, except for Hojo, since the bastard planned for that to happen "For Science!"

Basically everything that goes wrong over the course of FF7 is Hojo's fault if you trace it back far enough.
Jenova wasn't even really a threat anymore until Sephiroth went and merged with it, it had been sitting there doing absolutely nothing for decades even after it got dug up.

Sephiroth is the one with all the power and the primary threat, but Hojo is the schemer that set the whole mess into motion in the first place.
Bonus points for Hojo being Sephiroth's biological father and the one responsible for pumping him full of Jenova Cells in-uterus.

This is what happens when you embrace science unconstrained by morals or even basic common sense.