Further, Kiyoshi and his shadow giant is the justification I have for sending Sakura, Shirou and Aoi into the Nexus when I'm ready to do so, so taking him out means I have no justification for getting my characters there.
Have you perhaps considered the option of making Kiyoshi your "antagonist" submission, perhaps in the sense as an unwitting/unknowing one?
His power already sounds like the sort of thing that can drive that sort of character-specific sub-plot down its own direction, and lord knows that a literal child "villain" (here used loosely b/c I figure you're touchy on literalism) done reasonably well can provide for a tripped out kind of roleplaying experience w/ regards to how others end up interacting w/ him.