As you say, "part of our brains are wired for it." And it's clear in this show that the brains of the humanoid Cylons are wired for it too, and the Guardians worshiping a God suggests it was true of them as well.

Indeed, it is capricious (though I am not as sure about it being unnecessary or uneconomical) and that is the point. As the writers of the show have said, the Cylons had justifications, not yet shown on screen, for wiping out the colonies. The colonies were slavers, and though most of the slavers are now old or dead, they were part of the Cylon justification.

Imagine, as a hypothetical, that Israel had, in the 50s, acquired nuclear weapons and nuked Germany once it got back on its feet. An atrocity, to be sure, but nobody would have wondered as to why they did it, and many would wonder if they wouldn't have deserved it, at least a little.

(Biblical history is full of such atrocity of course, by former slaves against former masters (via their god) or even simply against people who made the bad choice to live in the land that some thought their god had promised to them. I don't think the biblical parallels are an accident, either.)