The Godmother...really didn't answer that many questions. It seems that the more powerful of a medium you become, the more they take an interest in you. Miko's junior would stare right at them all the time but they never attacked her, and the Godmother survived for quite a while and can't see the powerful ones. I have so many questions about the spirits. Why do the powerful ones eat the smaller ones?
The Godmother also didn't say what the shrine maidens actually want from Miko. Perhaps they want to drag her back to the spirit realm that they came from, or perhaps they actually want her to do some task for them. In any case, I can't see the Godmother possibly facing the creature that actually runs the shrine and produces the Maidens.