I think it makes perfect sense - but then again I've been doing Nishio-style aikido for some years now so I'm probably brainwashed
Anyway - Jaemin is on the right track. Atemi is not necessarily an applied punch in my understanding of the Aikido of Nishio Sensei. It's more like the position to strike - or the potential strike which is unleashed in a movement of the body instead of a punch with the fist.It IS a crime to down your opponent if there is any other alternative. Of course you shouldn't put your own safety after that of the opponent, but if possible use the atemi to show the opponent the error of his way.
The way I see it - the really tricky part is to let the atemi be a clear and present option - clear to both parties - without letting it turn into a threat.
To really cook your noodle I might add that I have heard Nishio sensei say that in some situations there is no other options than to cut your opponent. My interpretation is that you might have to use the atemi at hand to render him unconscious or even kill him, but it should be the last resort. The action will always have to match the situation.
Hope this helps.