Sephiroth, his own man or a puppet?

I don't think he wanted Shinra to stop mining Mako at all. He didn't care that the planet was being injured. His entire plan was to cause a massive injury to the planet, and for himself to be at the center of it so he could absorb all of the planet's life energy. He wanted to be a god, and it would have required the near-death of the entire world to accomplish that.