I feel pretty confident that Niall Ferguson, in his The War of the World, claims that Ataturk directly oversaw at least one massacre; I don't have my copy on hand, however. Also, the Armenian National Institute claims that Ataturk was "the consummator of the Armenian Genocide."

Also, Israel Charney (the founder of the International Association of Genocide Scholars) says:

It is believed that in Turkey between 1913 and 1922, under the successive regimes of the Young Turks and of Mustafa Kemal (Ataturk), more than 3.5 million Armenian, Assyrian and Greek Christians were massacred in a state-organized and state-sponsored campaign of destruction and genocide, aiming at wiping out from the emerging Turkish Republic its native Christian populations.