If ninja tools would had the capacity to seal gedo mazo, there would have been no reason for sage not to use them and to seal Gedo inside the moon. Analogy to physics: Chakra <=> Charge , Ninja Jar <=> Capacitor with huge capacity, Holy tree being the source of all chakra implies conservation of chakra, simillar to the conservation of charge (globally). Therefore the only known thing which can store the whole chakra is the the gedo mazo (the empty shell of the tree) which is equivalent to the universe (to store all charge). => The entire universe cannot be stored in something which is a part of it. => Sealing Gedo is not where it will go. I would rather go for assumption that in the end the tree (in one of its manifestations) will make peace with the mankind and will be willing to give the chakra and everyone will have be linked through the ninshuu.