Treatment of Mesopotamians

As I was eating my sandwich a thought occurred to me, prior to the Islamic conquest, Mesopotamia was a mix of heretics and infidels of varying degree to the Rhomans. Regardless of how such a thing would occur, how would these people have been treated as part of the empire should Mesopotamia had been annexed from the Sassanids.

If you were wondering, I'm focused more around early Justinian/pre-eternal peace treaty annexation than anything later.
 
First of all, its hard to see the Sassanids loosing Mesopotamia as it was their core territory and their capital is located in Mesopotamia. And if the Byzantines do conquer it they will probably have a hard time keeping it (Rome also left Mesopotamia a few hundred years earlier.

Now the ERE wasnt particulary religiously tolerant (in particular they will probably be less tolerant than the Sassanids, this depends on the Emperors in charge though) but in the end different Christian denominiations were somewhat tolerated (look at the Eastern churches). Mesopotamia will have a very large population though that isn't Christian. I am unsure how the Byzantine Empire would react to this, they dealt mostly with Christian-only areas.
 
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