Very Easy solution: Classify this type of meat manufacturing business as highly polluting and TAX it a lot until they become clean and green, ONLY then lower taxes. Yes short term it will increase meat prices, so what? Folks will be forced to eat more veggies which is a good thing.
To your point: I think the better mechanism isn't taxation, but regulation/fines. And there was regulation in place, but one of the points of the articles is that government officials in these areas 1- tend to be controlled by these massive industries and 2- push legislation to gut the regulations in the interest of "job creation" (read- increased corporate profits)