I agree with Pheonix, but I see where JonJon is trying to get at. I do think you are still overlooking Jenova's role in the game JonJon.
As far as the game's script goes (the only definitive proof really) I'm not. Jenova is used mainly as a plot device. Not once in the game does it EVER say Jenova is directly controlling anyone. The idea that she plants all the ideas in Sephiroth's head has no basis simply because there is no DIALOGUE in the game to suggest it. The entire villain element revolves around Sephiroth. Jenova is just what ties many of the things together (Sephiroth, soldier, the "clones", Cloud etc...). Like I said, she's a plot device, not a true villain. Where Jenova is a being who devours planets, so to speak, Sephiroth's goal is to become the ruler of the Planet.
By merging with all the energy of the Planet, I will become a new life form, a new existence. Melding with the Planet... I will cease to exist as I am now. Only to be reborn as a 'God' to rule over every soul.
Where does Jenova fit in? This doesn't sound like the plan of a being who devours life energy and leaves a planet dead. If Jenova has all this power people claim, why is Sephiroth in the picture at all? Why would she need him?
I feel the need to quote probably the best debater on the subject of FFVII, Issa:
Furthermore, Jenova is given a lot of credit by believers of the alternative theory. A laughable, ridiculous amount of credit. They paint her as some kind of 'master of control and manipulation', who just fools Sephiroth into doing her bidding. Do you want to know something? There is NOT ONE instance in the game where we know for certain that Jenova is directly controlling anyone... the theory that Jenova controls Sephiroth is laughable. It's a pointless over-complication that relies on every single person in the game being mistaken. Note - every single person in the game. That's a very bold, and quite frankly, arrogant assumption to make.
Is he wrong? No. There is NO evidence to support some of the frankly absurd claims of power people give to Jenova.
Furthermore, if Jenova is merely using and controlling Sephiroth, where is his justice? Puppet villains get their justice and forgiveness in Final Fantasy (Kuja, Edea, Golbez...) -- so where's Sephiroth's? He get mercilessly obliterated in the ending of FFVII, and there's not a jot of mention anywhere about "poor Sephiroth" being used by Jenova (since there's also nothing about Jenova controlling anyone...ever). The whole theory of Jenova "the true villain" simply runs rings around simple common sense and goes against everything the game tells us. It's downright wrong.
If anybody has any concrete proof stating otherwise, please feel free to prove me wrong.
^observe