How far involved was Mustafa Kemal Atatürk in the ethnic cleansing of Armenians, Greeks, Assyrians?

There are lots of good books on this. you can check out Zurcher’s “The Unionist Factor,” and a more general but still scholarly biography is Andrew Mango’s “Ataturk.” Part of the argument in those books is that Mustafa Kemal was able to lead the resistance specifically because he was the most competent, highest ranking officer that could be found with no culpability in any genocidal activities during World War I.
The massacres in Marash were awful, but not nearly on the same scale (5,000-12,000 dead). The Greco-Turkish War was accompanied by ethnic cleansing on both sides of the conflict, in a much more similar pattern to the ethnic cleansing done by all sides during the 1912-1913 Balkan Wars than the full scale genocide committed during the war. In the end of the 1919-1922 war, Izmir burned and a lot of people died. It is pretty contentious on who started the fire, but it is very likely it was the victorious Turkish army. In any event, that war was immediately followed by the Population Exchange, which had an awful human cost but is still considered to be a model of how to execute that sort of negotiated, internationally recognized population swap.

So did Ataturk have involvement in the Ethnic Cleansing of Anatolian Christians? I think its pretty well established that he had about as little to do with the 1915-1918 Genocide as was possible for an Ottoman army officer of his era. So in answer to your final question, he had far less culpability than the Young Turks.

How much should we blame Ataturk for the ethnic cleansing of the 1919-1922 War? The Turkish nationalist army was responsible for small scale massacres and ethnic cleansing. So was the Greek army. The nationalist wars that accompanied the collapse of the Ottoman Empire were very brutal and were accompanied by lots of ethnic cleansing. I don’t think the 1919-1922 war stands out much in this regard. The 1923 population exchange was probably about as humane a resolution to the issue for which one could hope. So considering the era and circumstances of which Ataturk was a part, I think Ataturk would have to be considered to be on the lighter side of the spectrum.