Yes and No...

I believe Sephiroth is controlled by Jenova but in a very indirect way. Sephiroth's goals in the game directly correlate to Jenova's natural instincts. Jenova travels and devours the Lifestream of planets. She's an exterrestial parasyte like Lavos in CT. Sephiroth is just acting on the part of him that is Jenova, his talk of becoming a god is just the human side of him rationalizing the natural instincts of Jenova that exists within him and creates the illusion that Sephiroth came up with this whole nonsense on his own.

Yes Jenova is basically brain dead in the game (though I don't necessarily believe she's gone consciously) and Sephiroth overpowered her will and controlled her to manipulate everyone into doing what he needed done. But I feel Sephiroth is indirectly controlled by Jenova's cells to fulfill her natural purpose. Basically it comes down to genetics...