The basic problem is that ag corporations are not financially incentivized to be humane to the animals
Just about any introductory class on animal husbandry will explain why this is not true. Animals that are abused (from their perspective, not our anthropomorphized perspective) increase the production of all sorts of stress hormones. These hormones cause animals to grow more slowly, get sick more often, produce less milk/wool/etc., delay rebreeding, and all sorts of other negative outcomes that are counter to what the farmer wants from an economic perspective. I won't pretend we maximize animal happiness, but we do try to minimize stress.
The problem is really that there clearly hasn't been sufficient effort put into making industrial scale farming also humane farming.
This may have been true in the past, but that is rapidly changing. Purdue University, where I got my graduate degrees, has a VERY strong animal behavior and welfare group focusing on commercial livestock. Many of the students who's programs overlapped with mine are working in industry on welfare programs designed to keep these very concerns top of mind. Won't say they always get their way, but a buddy of mine was just offer a huge salary to leave academia and design a layer welfare program for a large egg producer. He was told he'd pretty much get cart blanche to design and implement the program. He turned it down for family reasons, but I get the impression the job is his whenever he wants it. That is huge considering that Temple Grandin came to speak at Purdue while I was there, and she stood up and called the egg producers out on their unwillingness to even consider that their might be a better way. That was less than 10 years ago.
You claim that agribusinesses aren't being treated fairly (sometimes true) but you are painting with the same broad brush.
I don't believe that I am. I've found that there are a lot of animal WELFARE groups that are reasonable and earnest in their efforts, but there is a distinct difference between the animal welfare movement and the animal rights movement. The former is concerned with good stewardship, but practical enough to know that people will always want to eat meat. I consider myself a welfare advocate, and I have on several occasions objected when I've witnessed mishandling of animals. However, animal rights advocates seem to be far more concerned with their objective of complete elimination of animal use by humans to be bothered about being practical, honest, or fair. To be sure there are many who self identify as animal rights supporters who don't share that view, but in my experience that has been because they were unaware that there was another option. or that the two terms have different meanings.
You are right though, we have brought a large part of this down on ourselves by failing to engage with society as a whole.