I tend to just run away instead of fighting them to either their or my death. Then again, I'm usually only there for gathering purposes, and a fight would most likely kill me and not the chocobo
On a more serious note though:
I treat chocobos like I treat real life animals - being 'cute' doesn't make them safe. I eat cute bunnies and guinea pigs and duckies just the same as chicken or cows.
The no-food rule only extends to an individual animal because of a shared bond as my 'friend' (pet).
So ingame, I'd never even think of eating Jiro, my personal chocobo, and I kill everything that so much as puts a scratch on him, but all other chocobo are fair game.