I've killed many chocobos accidently (and some on purpose). The first time I was in a battle with one, I was didn't see it cuz the way the camera was angled behind a fiend. I just kept pressing attack and killed the 3 fiends that I could see. Then when they were dead I saw the chocobo and one of my characters was about to attack. I was like "Holy crap NO!!! Run little chocobo! RUN! But it was too late and the character attacked it and killed it. The time I killed one on purpose was because I was angry that the cat things in the chocobo place that clasko had kept killing me. As soon as one showed up in battle, I made all my characters attack it.