Kiritsugu probably made the right decision in this situation, but the last scene in the episode also showed that he is batshit crazy at the same time. You have to be a psycho to not have to think twice about pulling the trigger in those kind of situations. Clearly something broke in his head, after the whole Shirley incident. This is what gives rise to lack of hesitation, which Natalia considers to be a rare talent for those in her line of work.