The Keyblade War was, as far as I can tell, not necessarily fought between Light and Darkness. It was just the Keyblade Wielders killing each other off in the hopes that their fighting would allow one of them to forge the X-blade. It's never stated, but to me that implies that there was a lot of manipulation and backstabbing going on a la Game of Thrones, hence why Cyrus's backstory is the way it is (he was introduced to war via manipulation by one of the more experienced Keyblade Wielders, at least until Cyrus got wise and started fighting for himself, becoming the Grimm Reaper).