How do you even know that? Text says they were armed with knives. And what do you mean "civilians" in this context? The article lists them as armed belligerents.
Well, I'm going by what the Wikipedia article says, that they were "Atahualpa's counselors, commanders, and unarmed attendants". According to the article the "armed host" was stationed outside the city and fled when the emperor was killed.
Edit: sorry, captured, not killed.