also, here is why the mage's specifically are not alluding to the gay's plight or jewish oppression. If that was actually the case, then they would also have to be considered as the cause of the blight in the world. I don't think that is a statement that Bioware would want to make.
The mage's are taken and secluded from the rest of the world because, historically speaking, unchecked the mages caused destruction and mayhem on mass scale. Creating the blight and dominating the land.
You are certainly entitled to read the story any way you want, but I am very certain that this plot thread was not meant to be read in the way you are interpreting it.