Discrimination of Magic people against Non-Magic people is due to superiority complex, as more and more people gain access to magic through breeding in specific ways, the non-magic people are dwindling. The War of elimination at this point is pointless as the non-magic people are dying out, or more closely explanation, nature adapts them.
The actual problem is between elite Magic and non-Elite magic people, which is noticable due to the MC being barely magic.
The explanations are not crucial but you will not understand a few things later on.
The actual problem I see is that some people think that heavy offensive magic is more important than a subtle magic set of abilities that will yield the same or better results in open conflicts.
The MC has a clear advantage, even though his magic is inferior.
Over the course of the show you will get to know that it doesn't matter what magic one has, if he knows how to use it effectively.