So, your theory suggests that unless and until the Chakra is not eradicated - albeit indirect allusion - Kaguya will remain connected with people one way or another? I will have to agree, and I don't think it's a theory. It makes perfect sense. Kaguya is the original being, a vessel that started Chakra amongst humans.
As long as it remains, so will Kaguya's will. Which is why I believe that the Juubi will be destroyed or transported elsewhere along with the Bijuus, ending Chakra and finally bringing peace.