Kiritsugu is... not the greatest at thinking ahead further than 3 seconds if the topic isn't Killing Mages. A reminder that he's the one who deliberately taught Shirou how to do magecraft wrong, hoping that the boy would just give up because it was painful, and underestimated how stubborn Shirou was by several orders of magnitude.
An explanation: It is not supposed to hurt when you use magecraft. It did for Shirou because Kirtisugu taught him to use his actual blood veins to channel the magic instead of, y'know, the magic circuits that are meant for that.