Meh, I don't see that there's enough to form a basis stating that the Mystic/Guardia war was already in effect. I mean, obviously the Mystics were still on their old turf in that mountain near Truce. So that just makes me think that the war wasn't going on yet if nothing else tells me anything at all...
Plus, all of that Janus stuff is just speculation...For all we know Janus got fucked up and the Mystics captured him to make him dance for them at nighttime (or to eat him...w/e) and then magic happened...Or hell, maybe Janus just escaped Ozzie, and eventually found humans and later on, learned magic, decided he didn't care for humans and then joined the Mystics...
Heck, you'll find TONS of these meaningless theories on what Janus did and how he finally got his magic by reading any of the countless Magus fanfics (although my own hasn't gotten into that history of Magus yet...but it will in a chpt called Advanced History).
Also, about the Mystics...We don't know if they were ALWAYS called Mystics at all...Perhaps WHEN they learned to use magic they were dubbed Mystics...Who knows, yar?