I really think that the only thing Jeph could do to make Corpse Witch's alignment more obvious is to have someone standing on-panel with a sign reading "Boo! Bad 'Bot!" whenever Corpse Witch is featured.
As for Jeremy, we're just being reminded that Corpse Witch doesn't really do 'employee feedback' except when it's self-confirmation (and silence will do for her). She didn't really want an answer and, even if he did something like yaw his optic back and forth as if he were shaking his head, I suspect it was disbelief and disgust at her rather than saying that she isn't too smug.
People who think that they've got it all figured out are usually the ones who are the most surprised when they find that, as Bubbles put it in panel 2, that the leash has snapped. Of course, that's another clear warning that Corpse Witch seems to be ignoring in her certainty that she's won.