What's the big deal? It's just there to prevent a logical gap for things like the War domain bonus and the Spiritual Weapon spell. Sure, the former isn't obviously relevant if the god doesn't even use that domain, but what the the spell? You could just say that spell is banned for that god, but then that opens up another massive can of worms. It could result in lists of banned spells for every single god, which brings things right back to the 2ed system.
Besides, I can't imagine a god of absolute pacifism working in the core rules anyway. Against humanoids, sure, and I can even see it against traditionally evil races like orcs, drow, beholders, mind flayers, and so on. But what about when the hordes of undead invade your village? Even the peace-based Vows in BoED have some exceptions, undead included. And even if your Yunitee worshipper refuses to even thinking about harming the hair of any living thing, regardless of how eager it is to kill you, when the skeletens burst, in, what's wrong with breaking out the greataxe?