I think it will come down to the hypocrisy of their programming (established in part one when they criticized humanity for genocide before being exposed as far worse), and their ability to override it. Isaac talked about his ability to modify his own programming in his Big Romance episode. Pretty much all episodes of Orville have had a TOS-like moral to them, and we don't really know what the message of this story is, aside from "it's bad to kill people and stash the corpses in your basement." It seems likely that the theme to this one, especially given the title, will be about identity politics-- everybody not like us must be eliminated-- and that the Kaylons will learn that they have become what they once opposed.1. Similar to the robots in Voyager Prototype, or Kryten on the Nova 5, maybe the Kaylon are still absently servicing their long dead creators or restricting their expansion to guidelines set down by their old masters? These duties may be so deep in their code that they don't even realize that this is a bunch of tasks that they do not have to do, and if they did figure it out, become aware, they are slaves to their own code and can't disobey. This is why they have humanoid bodies and cities with rooms and doors.