I think there's an interesting commentary on power dynamics. A major question is why the mage class isn't in the higher echelons; mages can reproduce, so why shouldn't they be in a position of power? I'm sure it'll be answered soon; possible theories include the controlled reproduction of mages under state surveillance or that the birth of mages is more arbitrary than direct lineage. Either way, if I were a 'regular folks,' I would have good reason to be wary of mages. But the suppression of mages under their system is also antagonistic to 'regular folks, ' as seen by the forced betrayal from Lovi. A system that forces you to act like Big Brother in your neighborhood serves no one besides the state. It may seem like killing Lovi's entire family was contrived, but the logic behind it was to strike fear. Report the mage, or else you and your loved ones will die too. This way, the regular folks are threatened by the system that is supposed to protect them.
This wasn't very subtle; the bureau directly states that magic isn't inherently an issue. The problem arises when they lack a monopoly on magic. It's funny that magic is so dangerous that regular people shouldn't be in contact with it, but conveniently safe enough in government facilities far away from civilian eyes.
I don't know how you can be bothered by homosexuality when the premise of the first chapter is why bigotry is wrong.