I think Jenova has Sephiroth so brainwashed it doesn't really matter who's calling the shots, because even if Sephiroth is the one in power, he's doing more or less exactly what she wants him to. Even after Jenova is supposedly "defeated" (although it's not clear whether she actually is or not), there's no reason for all of her brainwashing of Sephiroth to come undone. He'd continue going for godhood without her help.