Here is my take on Sephiroth.

He was an individual, he made his own decisions, but those decisions were influenced by Jenova's presence in his body. Just like the genes of your parents can influence the way your personality develops. The difference is that Sephiroth's mother was a psychotic, cosmic demi-god with a desire to destroy everything in existence. That kind of genetic structure is certainly going to provide more than a normal amount of "influence" for Jenova to wield over Sephiroth.

Let us also not forget the "reunion" theory. All of the former residents of Nibelheim, including Cloud, were injected with Mako and Jenova cells. Sephiroth showed an ability to not only influence their decisions, but to also control their actions consciously. If Sephiroth can do that to a bunch of people with a few Jenvoa cells in them, think of what Jenova could do to Sephiroth, considering the fact that half of his genetic structure is made of Jenova cells.

The counterpoint is that Jenvoa has lost a lot of her former power. Hence the reason she can't outright control someone as powerful as Sephiroth. One way or another, she was most certainly influencing his decisions, subtlely guiding him down a path of wanton destruction. He was making his own decisions in a specific manner, but Jenova was making the big, huge general decisions for him. He decided to use Meteor to injure the planet, all she wanted was for him to wreak havoc. Didn't matter to her how he did it.