Sure the Turks may have done bad things to Greece people and similar can be said to the Roman before them. The same can also be said to the Greeks people when they're expanding their once great empire. I'm pretty sure the Greeks at some times committed some atrocities in large proportion when they were conquering other nations that you are not aware of. The same can be also said to the British and French empires, etc.
Having said that, about century ago there were a huge exchange of residents between the city of Istanbul and Thessaloniki. According to the an architecture history book that I've read some times ago (cannot remember he exact title now), essentially you can find more Greece people is Istanbul city and vice versa i.e. more Turkish people in Thessaloniki city. As you probably know the fact that one third of Greece people is living in the urban area, the number of people moving in these two directions probably quite a lot, albeit a rather smaller scale if compared to the later India and Pakistan residents exchange movement.
This fact is kind of proof of the seamless integration and the tolerance of the Ottoman empire until of course the fanatic of the nationalists from the both sides taking over with their own propaganda. Imagine if at one particular time in European history that you have more Italian people living in Munich and more German people living in Milan during the period Holy Roman Empire period. It's kind of unthinkable now but that's really happened during the time in Europe few centuries back and the melting pots nature of Ottoman empire probably has only been surpassed by the modern USA.
p/s: there is probably no original Turks people in Turkey anymore since they are the mixed descendent of the various people that lived in Turkey namely Turkic and European peoples including Greece.