Eh, more of a deconstruction of the 'kill first ask questions never' mentality of many rpg's, only like, 5 enemies in the entire pacifist run actively want to kill you, the others are just unintentionally harmful.
If you went around just murdering random people it wouldn't be ok.
Though I'll admit undyne is a play on the fight or flight response, and maybe should have been a bit more obvious.
basically, it asks the question of 'why are we fighting?'
"just because you can, you think you have to"