If Mystics were humans before it makes no sense that there's a war going on between the two different kinds.
... Yes, it is very silly for humans to be having a war between themselves.
But seriously, ethnic wars are hardly unique, and Sci-Fi/Fantasy is full of stories about humans being at war with near-humans. Heck, there have even been suggestions anthropologically that early humans were at war with other early humans.
And saying that they mutated from the Zealians is just too big of a leap to take seriously.
Not mutated, and not from Zealians. Evolved humans. Presumably they would share a common ancestor, with one branch evolving into the mystics and the other evolving into the Englightened Ones. The Zealeans are already essentially mutated humans (they have magic, in case you didn't notice), so why should additional mutations be a leap?
Why would Zeal have any survivors, and why would they reproduce and turn into Mystics, and go at war with the humans?
Well for one, Zeal did have survivors. We see them in the Last Village, but that is besides the point since we saw Mystics on Mt. Woe before Zeal fell. Thus, the survivors of Zeal are different than the Mystics. As for why would they go to war, why does anyone go to war? Limited resources, national pride, racial tension, etc.
And why would they treat Magus like some kind of god?
Why did the Romans treat Julius Caesar as some kind of god? Great leaders have a tradition of being deified.