Again, Violet literally eats her opponents (her arm absorbs them and nourishes her with the energy it gains). Then you also have stuff like Shadow Hearts where you'd accumulate malice from fights and collect the souls of the fallen enemies. There's also Suikoden that occasionally give you the choice to execute characters (i.e. Kwanda), not to mention the giant wars you take place in.
I just see it like any typical video game: named characters / NPCs = important and you should care about them; nameless bandits = fodder. If this were a more complex show that was trying to explore in-depth how an iseki world would actually work and what Shun's tax policy is I'd probably agree with you. For now its about a spider girl leveling-up and trying to find the tastiest food. For me, outside of the yet again boring human parts, I was fine with the episode.
That said, later on, once Kumoko joins up with the demons I think this line of thinking becomes far more appropriate as she starts to become the cause of death for, well... not just faceless bandits and assassins trying to kill families and kidnap children. The manga hasn't gotten that far yet, so I'm curious to see how they'll treat Kumoko dealing with that sort of stuff. If she continues her fairly non-nonchalant "don't care, got EXP" stuff then it'll definitely be a problem. For now, though, I have no problem with her killing nameless bandits and assassins while giving it no thought.