I think Gunko knows that Imu can and does do that to her. But, I don't think she's "awake" while Imu is doing it. Once Gunko wakes up, I doubt she'll have anything but a vague memory of what Imu did while possessing her. It'll be like a dream she can't really remember.
Maybe that's why her memories of Brook are so spotty. Imu might have possessed her the first time, in order to kill her father with her body, for some reason. It's just that the memories are mostly gone because it was all like a dream to her.
Because...we gotta keep Gunko relatively "pure" if Brook is going to end up rescuing her. If she's our "princess" for this arc (or a future arc), she really can't be fully culpable for the crimes she committed. That way, it's not really much worse than Doflamingo controlling people with his strings. Gunko knew about it...but didn't actually "experience" any of it firsthand.
Gunko probably did give Imu "permission" to possess her. If only through some sort of deal. But, she probably isn't aware of the full extent of the deal she made. She isn't fully aware of the consequences...probably.