...Kind of murder billions of people?
The sundered were not exactly murdered, simply rendered into 14 shards of themselves that all end up living new lives on an equally sharded world of their own. You can argue that this act certainly did end one life per sundered if you view it a certain way, but the reality is they weren't exactly "killed", thus murder is not the correct word. It'd be different if the sundering snuffed out each and every one of those lives. Instead, she essentially diluted lives into a glob of water and splattered it all over the place to exist all over the universe without any memory of the original droplet it started from.

But the main differences is that it's Zodiark's people that start the war
And where did you hear this?

Last I remember, the Ancients concocted a plan (after being 'kinda-saved' by Zodiark) to nourish the world and then sacrifice life born through that new power to re-create those who were initially sacrificed to Zodiark to stop the calamity in the first place. Think of it like sacrificial recycling. However, certain Ancients did not agree with this plan, thus they split from the group and performed a similar sacrifice to summon Hyde - a Zodi-Counter. I do not recall ANYTHING being said about Zodi-worshippers instigating a war with the other group, only that a new faction arose to create Hyde, who eventually sundered the planet and all but three inhabitants. A lot of these details often boil into he-said-she-said with our only source of (potentially) correct information coming from the horse's mouth itself, Emet-Selch, who is happy to point out that Hyde might be inclined to convey a completely different story to what he tells us. In short, we'll never really, REALLY know, but for the most part it wasn't so much a civil war, rather than a hidden portion executing their own plan.

At least, that's how it was to me. As said, I saw no mention whatsoever of those groups actually 'fighting' eachother. Emet simply refers to them as foolish nay-sayers who followed their own path and caused the divide.