That trick would have worked 2 years ago (when this thread was started) because back then you only got a major warmongering penalty for exterminating a civ, and a minor one for declaring war.
In BNW the "I'm gonna wait for them to DoW me and take all of their cities except one!" doesn't work anymore, because now you also get a minor-major penalty for each city conquered. So if your opponent has 4+ cities you're gonna get a lot of hate for taking them all whether you end up exterminating him or not.