See, I always figured the war was some kind of distraction. Or some kind of excuse to build up his fortress and power and whatever exactly he needed to summon Lavos. It's all speculation, but you could easily imagine a backstory where he has a bunch of requirements, basically requiring him to amass power to fulfill them, and he doesn't care if alongside there's a war or whatever.
Regarding Ozzie, Slash, Flea, waging war along side him..? Seems like their loyalty was tentative at best. It's pretty easy to imagine them, once Magus disappears, following suit, thus abandoning the war effort.