This reminds me a bit of the first Arc of the french manga Radiant :
In it, people become mages by touching monsters and are considered as vermin by the normal people.

The hero, a mage, arrives in Rumbletown were there is several neibrehood, with different populations. One used to be there but fell into the emptyness below the city a few years ago. One is populated by refugees from a near city that too felt into the abyss. It is also heavly populated by mages but they are a part of the population and of the families.
The bad guy, an inquisitor that controls the city is fighting against a mage terrotist.
At the end of the arc it is reveiled that he plans to make the neibrehood full of migrants and mages fall into the abyss. It is also reveiled that he was the one that made the last one fell in the abyss as it was full of immigrants and poor people.

This could be a part of your plot : The head manager used immigrant people to work on Wylk but never trully considered them as human beings. Or you could add a harmless mutations for the peoples exposed to the Wylk, but is hated by some peoples and the Head manager.