I'm essentially on the same page as you. If I'm not following my zoning, I'm in the wrong. If I am, then I should still be expected to keep the animals in a healthful way. The only concern is where "healthful" becomes subjective. People can find problems where they want to. Conversely, people...
I've taken a liberty and tried to condense/classify OP's stated reasons against; my classifications in bold:
Smell, flies, rodents (sanitation)
noise (annoyance/human quality of life)
pollution (chicken 💩), run off from poultry, Death loss disposal, disposal of in trails when harvesting...