I do understand that the historical consensus is that Mustafa Kemal did not have a direct involvement on the genocide of Armenians (as exposed in this previous thread), and that his population exchange of Greeks was "mild" in comparison with the crimes in the the Ottoman era. This site, however, claims that Kemal had a direct involvement, even if understandbly biased as it might be. Also I do believe that Atatürk sought to make Anatolia the natural homeland of the Turks.
In resume: Atatürk did nothing wrong (or at least not comprehensively so), or is he to be held responsible for the crimes commited in Anatolia in the same level as the Young Turks in the late Ottoman Empire?
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 two events your second link reference are outside of what I think most scholars would consider the Armenian Genocide proper, which occurred within the confines of 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.
I don't have enough knowledge about sources that document the level (or lack of) Mustafa Kemal's involvement in ethnic cleansing. However, I can say a few words on "Also I do believe that Atatürk sought to make Anatolia the natural homeland of the Turks." This will not directly answer the majority of your questions, but should help you understand where Mustafa Kemal stood politically with regard to ethnic groups and nationalism.
Ottoman Empire was a big, multi-religious and multi-ethnic empire. Kemal's main goal was to save and establish a part of this crumbling empire as an independent state. His idea was much closer to a nation state than a multi-ethnic empire, and the nation in this nation state would be the Turks. However, he was influenced by two separate past ideologies: older (and never very popular) Ottomanism (accepting all ethnicities in the empire as equal citizens with equal rights and importance) and newer Young Turks (Turkish nationalism). The way he synthesized these two was:
a) He considered himself a Turkish nationalist ('Anatolia as homeland of the Turks' idea is fed by this, and nationalism is one of the 6 "arrows" of his ideology, Kemalism)
b) "How happy to the one who says I am Turk", motto of his republic -- This means that "Turk" is defined by self-identification rather than race/ancestry/religion/etc. (This is the influence of Ottomanism, which said whoever defines themselves as 'Ottoman' are all equal).
This means that if a citizen has Greek ancestors but lives in a community consisted mainly of Turks, and identifies herself as part of this community, Ataturk's nationalism has nothing against her. Think Russeau's social contract, not unity and power of an ethnic group. Another quote: "The folk which constitutes the Republic of Turkey is called the Turkish Nation." The constitution says "Every citizen is recognized as a Turk, regardless of ethnicity, belief, and gender, etc." This is a national identity built upon shared values, history, and language. It does not require racial or religious unity, and is open to different ethnic subcultures, as long as they see themselves as branches of the main (Turkish) national identity.
Mind you, this idea based on shared history and social contract is still labeled as 'Turks' and 'Turkish nation', and it isn't full-on welcoming to people that proudly express their identity as Greek, Armenian, Kurd, etc. It does not have space for languages like Kurdish (while race and religion are not a required part of this national identity, language is). Especially right after the harsh Greco-Turkish war, hostilities between Greek and Turkish ethnic groups were at an all time high, and Mustafa Kemal did not hesitate in removing a significant portion of Greeks through the population exchange. However, that exchange was carefully executed with minimal possible damage to the people involved (still high, of course, given the nature of it), and Mustafa Kemal's nationalism is milder than the full blown ethnocentric nationalism of the Young Turks.
Sources: