I agree with killing murderous brigands, highwaymen, and other such bandits in self-defense and also in protecting other potential victims. But I can't agree with the author having the MC, Mitsuha, use the justification of "they're not human" in order to rationalize the killing of those bandits.
The first step on the road towards genocide and inhuman cruelty is to dehumanize others.
"... They're not human anymore. As in, it's fine to exterminate them."
That says it all really. It's probably that very same thought process which led the Japanese to do many of the cruel acts that they engaged in during the Pacific War. The same is true of past genocides committed throughout history by other cultures as well. It's a slippery slope.
Best to acknowledge that the bandits are human, but if you need to kill them in self-defense, then so be it.
Well, that's enough preaching from me, for now.