Well, Jinpa says: "You see, it's customary to maintain a level of separation between those who've taken a life, directly or indirectly, and those who have remained spiritually pure." Kyoshi reflects that Kelsang saved the lives of countless villagers by killing pirates, yet was treated as unclean.
I believe that self-defense is also included due to the "directly or indirectly" line. Might be a stretch. Anyway, one should also not forget that about three hundred years passed between Kyoshi's early life and Gyatso's time. Philosophies change. In fact, the novel's chapter 1 mentions that the Air Nomads had become extremely detached from the world by Kyoshi's time. Jinpa was also treated as a oddity among his peers due to him managing the temple and its economy instead of focusing on enlightenment. By Aang's time, the Air Nomads actually appear to have taken greater interest in world affairs and non-spirtual matters.
Indirectly killing someone could also be not helping someone in need when you know you can and your inactivity will result in their death (like in modern times not calling an ambulance for someone who's been beaten to near death). So I do think dragging self-defense into that may be too much of an assumption. Self-defense nearly always changes things.