Weswin is right.

It is largely a game balance issue. If we weren't fighting each other there would be wholesale ganging of scions going on. That's not a lot of fun for those who like a challenge or those who get ganged repeatedly. There is no reason two groups who both have the best of intentions cannot be at odds with each other. And yes, you're right that if scions became all powerful again, warlocks and sylvans would likely forgive and forget (except for conjurers being hunted) and go back to having peace again while they fought the scions.

If a war is necessary to keep the game entertaining, and plausible (which the sylvan/warlock one is), then the cost of "broken friendships" between the warring cabals is perhaps acceptable. The two were not supposed to travel together anyway in the first place.