look
the term Greek Muslims was used obbiouvly so they wont seek any claims to self-determination or special rights, the way the Turkish Cretes had done in the early 1900s which led to their expulsion from the island after the first balkan war.
so some may see it as a negative thing but it also assured that these Turkish Greeks or Greek Muslims would remain safe in Thrace regardless of what happened because they are Greek. Don't forget this happend in 1922.
either way all these populations have assimilated into the Greek lifestyle and the only thing theyve majorly kept is their religion, so they really dont care about political isssues as long as they are free to live their lives.
and yes they wre discriminated in the 50s the same way the greeks in istanbul were thanks to their cypriots "brothers" who decided to wreak havoc but this is no longer the case.