Would it be ethical to grow meat in a vat without a brain associated with it? Personally, I think pretty clearly yes.

So breeding suffering out of animals would seem to be between growing meat in a vat and what we have now. So it would seem to be a step in the right direction.

We, and animals, almost certainly have suffering because it had survival value for us and animals in the environment in which we evolved. Being farmed for meat is not that environment. I don't think removing suffering from our farmed animals has a downside. Of course, removing it from wild animals would probably not be a good thing, but would probably correct itself relatively quickly in the failure of non-suffering animals to survive.