You do bring up a good point. I've taken only a few introductory and beyond courses for psychology, so I have a basic understanding of conditioning.
If left up to the owner, often times, they may unintentionally negatively condition their pet. A lot of pets are as smart as you say, they typically learn the right thresholds, and repress their instincts as much as possible because they know nothing good will come of it if they're treated that way for long enough.

But in conjunction to that, or rather, due to that, we must be able to interpret our own pets emotions much better than we would of even our own friends. One great indicator is obviously what a lot of people have been stating, the tail motion, the swinging arms, and the constant meowing.

Look at her ears, her eyes, and the jaw position. If she were conditioned into this, her ears would be much flatter, which is highly common in "conditioned," or for a better word of what you've described, traumatized cats. Her body would be closer together, and her pupils would not be as dilated. This is why we can joke around about her being dramatic—We can't understand her completely, but neither can she understand us.

Sorry for the really long reply, but you seem like you have good intentions. I like that you brought up a lot of points that pet owners tend to ignore, but there are also a lot of things that people ignore that some owners don't. The owner had said not just certain that the cat isn't being hurt, but *harmed*. This means, sure, she might get annoyed at us, but honestly, what's the harm in that? We have pets to have companions, not to worship them. We give them love, and we annoy them so that they can do that same back.