I've only KOed a few Audino when playing my friend's file to level her Pokemon up. I do feel bad; such sweet little things yet they just have to be Public Enemy #1 for EXP fodder. Yet I still jump at the chance to get EXP from one... N would be disgusted with us.
Also, even if they are "just pixels", there's nothing wrong with feeling sorry for them (or sentimental value for your own Pokemon for that matter). They try to make games emotional, even if the characters you grow to love aren't real.
On a side note, I just bet someone is going to write a creepypasta of all the Audino they ever "killed" coming back from the dead to haunt them.