Sephy didn't control all of Lifestream. Maybe about 1/2. This is my reason why:

In FFVII, Sephy said he wanted to use Meteor, not to destroy the world, but to leave a huge dent on it. Then he said Lifestream would come and heal that part of the planet, so he could absorb Lifestream's power and become a god. If he did have control of all of it already, he would have already won.

I'm not too sure about AC though, because he did use Geostigma to corrupt it, but it didn't really go much further than that. After all, the movie was mainly about Cloud and his own problems.

One thing I'm also not sure about is if Aerith controls some portion the "pure" Lifestream. I know Lifestream is controlled by the planet, but I'm thinking that maybe she does too, because in the end of FFVII, after it shows Lifestream gathering around Holy to stop Meteor and then shows Aerith. I'm thinking it means that she was the one responsible for that. And in AC, she also cured Geostigma and purifying the Lifestream which Sephy tainted in the end of the movie.