finally a valid arguement. I might just shut up now. Oh wait:

uh...Jenova never died. She was sealed. Then she was found by Shinra. Her head was taken by Sephiroth. Her body escaped from shinra. Jenova had the ability to live in separate pieces, but these pieces would eventually return to the head. These pieces include the body and the cells injected into humans.(Which explains why Sephiroth, who had jenova cells in him, went crazy took the head in the first place)

It is clear that Jenova has the power to manipulate those with its cells inside them. Whenever Cloud became close to Jenova (usually disguised as Sephiroth), he did some terrible things, like hand over the Black Materia, beat up Aeris, allow Aeris to be killed, you get the picture. What I don't understand about the "Sephiroth is the true villain" idea is what gave Sephiroth the ability to use this manipulation power rather than become subject to it like Cloud.
You've got the idea, just backwards. It was Sephiroth using Jenova's cells injected into the 'clones' to control them. This includes controlling Cloud to make him give Sephiroth the B.M. And Jenova was killed, the remaing Cetra killed it and threw the body in a chasm. Sephiroth can also control the cells of Jenova, (keep in mind that he is part of it, so to speak). So, yes Jenova looked like Sephiroth, but only because Sephiroth, who's controlling the body of Jenova, is making take that shape. Yes, Jenova did break out of the Shinra building, but it was Sephiroth making it do so. Jenova is throughly dead, but Sephiroth is controlling it.

I've practically written an essay on it, which explains more.