I can buy the religions revolving around the magic format, but not so much the persecution.
Some religious prohibitions and encouragements certainly are very illogical. For example, the rules in Leviticus, though following them helps with spiritual cohesion and honours god, aren't perfectly practical, and religions that allow you to commit suicide for your god also don't strike me as being fun to follow. But religious rules still need to create a viable society or else that society and that religion won't last very long, and it seems like powerful war mages would be too much of a competitive advantage for the elites to agree not to use them for religious reasons. Maybe there's a downside to the other types of magic, or an environmental/genetic aspect that makes the empire-born Light/Shadow mages powerful or common enough to get away with persecuting the other ones, or something else that explains the reason why they became an empire while swearing off a significant battle advantage? Or the persecution entails forced military service?
The mind and emotions don't have to be viewed as distinct from the physical; our mind and emotions can be viewed as springing solely from our physical reality. For example, it's hard to use our mind when we're in pain, or suffering from a physical mental illness. We don't have to consider the mind and soul as another "us" completely separate from our bodies; it would be possible to view all the elements as interlocking rather than four physical and two mental. I'm guessing fire, water, earth, and air as the other four? In that case, Shadow/Earth/Water could be set against Light/Air/Fire as more "grounded" elements against 'higher' ones for a three against three division.