While those particular kitsune do disappear after defeating the Alraune, their content is mostly unrelated to Kiyoko's; the only difference it makes is that helping them changes their interactions when you meet them later in the Kurokawa Kitsune Den dungeon. You need to complete the Den before you can free Kiyoko from the Astral Plane, and helping them allows you to avoid fighting them if you also have the Amulet of Transference/Union on you, but avoiding the fight has no effect on freeing her.
Actually getting Kiyoko only requires exploring the ruins in the south-east of the Old Forest, which can be done at any time if you haven't done so already. Make sure to neither get disgusted by the orgy mural nor throw away the amulet, since doing either of those will lock you out of Kiyoko's content permanently. And until magicocks are implemented, you'll need a cock to progress her storyline.