Bah. I think she had full control, always did. Yeah, her headless body might need guidance, but her head can do that. I think Sephiroth, after he went insane, mentally submitted to Jenova's will. He called her his "Mother" and an Ancient. I think he would've willingly obeyed her every command.
Kishi: You still haven't explained how you think Jenova's body escaped.