One, the concern about disease wouldn't be so great if the animals were raised in a sustainable manner. Like jails and college dorms, when you get a lot of creatures jammed together in a small place, disease outbreaks are more likely and more severe.
Two, another reason commonly given for the "security" is a fear of "bio-terrorists endangering the food chain." Less centralized production would probably be a better safeguard against terrorism.
That is why I mentioned that the security things were beneficial conditionally. I agree with you fully. It is just a bad idea to put so many living things in such a limited space.
Three, I suspect the real reason for the security is to prevent consumers from seeing photographic evidence of the conditions in which their food is produced, and also to cover up the environmental crimes being committed by the CAFO operators.
The operators don't really have much leeway the way things go, environmentally speaking. They are limited to a certain number of animals and have certain resources to use. They use the lagoon waste on their farmland to fertilize it and such. At least in my area, which may be different elsewhere. These places aren't good for animals or the environment, but in all honesty they are what they are.
And a point about the humanity issue. I'm not ethically concerned with the way the animals die. I'm concerned with the way they live.
If it makes you feel any better, working in breeding in order successfully inseminate the sow there must be foreplay and sexual arousal for the semen to take. This requires a fair amount of bouncing and nipple rubbing while sticking your arm up the sow's bit's. Let's just say, it is a well payed job...