They aren't dead, they are unconscious. They voluntarily passed along their Tama energy to Musubi, who used it to jump-start Minato's "Ashikabi core" which the Jinki had drained. Then she took on all the energy of the other Sekireis that were left on the island (it hasn't been revealed if she also received the energy of the Sekireis back at MBI or hiding outside Shinto Teito) and transported Minato and herself up to Kouten to face #00.