one of the great things about VII is all the theories and debates over them that last until the present day, unfortunately, I believe one of the writers (Kitase/Nomura/Sakaguchi/Nojima) clarified that sephiroth was controlling Jenova.

I'll still always believe that it serves as a scenario similar to FF's - it was the will of darkness that compelled Garland & the Fiends, the Devil that ended up controlling the emporer, zemus controlling golbez, the void overcoming X-Death.

My belief is although Sephiroth was acting of his own free will, with his own intentions and inclinations, it was still the overall general will of Jenova that he was carrying out. Finding a way to become ruler of the planet, as so far as to 'become one' with it. Until it dies and he/she/it/they must go to a new one in order to survive, repeating what started 2,000 years prior to the game's scenario. I believe that's the function of Jenova.