Well mostly cause no matter how deranged this monster is he still consider Jenova as his mother. The father was Hojo the mother was Jenova and the female scientist was nothing more then an incubator.

Like you said he only freaked out when he found out !
He found out they abused his real mother.
He found out they were abusing of the planet that he beleived should belong to Jenova.

Of course Jenova had some influence.
Just like any children get influenced by their own parents.
Like i was pointing Jenova brought the mean.
Sephiroth didnt care how it was done as long as he would get revenge+stop the ppl from abusing of the planet and survive.