Well he did hide that thing inside of her and the gigai was designed to actually limit her spirit powers not heal her as she had hoped. If i remember correctly with time it would have turned her into a normal human being.

And yes I believe that the gigai helps them recover spirit energy. But think about it, isn't it better to have them actually interact with the real world that just be unseen by everyone around them. I could only imagine what is going to happen given the personalities of each character.