Honestly, if Greece does take Constantinople and there does end up being a population exchange with Turkey, I expect there to be an expulsion of Muslims regardless the effect on the city. This happened in Thessaloniki, why not the ancient Greek capital?
This expulsion will definitely hurt the city. Quite frankly, if Constantinople does not remain the natural destination for Anatolian migrants, I expect the city to never recover anything like its former stature, that it would just be a regional centre like Thessaloniki. Constantinople will never be as big as Istanbul.
The Greek population of now-Istanbul, along with the Greeks of adjacent islands in the Marmara, were spared the early 1920s population exchange, in exchange for the Turks of western Thrace being allowed to stay. The Greeks of Istanbul left only after pogroms in the mid-1950s.