So you just turned an entire population into slave labor? Oh, that's not an atrocity
As some other people have said, the UN right now isn't very well developed, except as a means to win diplomatically (not a very fulfilling way to win, either). Perhaps, if the UN feature is expanded, razing cities could become an atrocity.
In the ancient, and middle ages, razing a city isn't really an atoricty - it's standard practice. So in these ages, razing a city would only affect the city's former civ for reputation. However, with the advent of the UN, there could be an option such as "Hold Geneva Convention" or "Establish War Crimes Tribunal", which would effectively make mass genocide or enslavement an atrocity which would severely drop your reputation with all other civs.