All true Northie, I know it's not an easy-answer situation, and once you start involving economics-driven livestock husbandry practices, particularly those in massive commercial operations, it's nigh-impossible a situation. They're one of the largest bastions of development of vaccine/ antibiotic/ drug resistant diseases. They're in large part responsible for the severity and virulence of so many modern diseases, as a byproduct of their modus operandi. (Though some backyard breeders and farmers are certainly doing their bit to contribute to those resistant strains of diseases... It's gobsmacking how heavily some folks medicate and vaccinate. Understandable though, especially when pets are involved.)
Over time, it seems these commercial operations will likely end up having to breed for resistance, judging by the past enormous losses they've sustained which even vaccination/antibiotics etc couldn't reliably prevent, and their past projects in breeding programs aimed at disease resistance. They know it can be done, though they'd have to accept lower production for a while to achieve it.
The final straw that looks poised to break the camel's back is the upcoming changes to regulations about antibiotic use due to the growing epidemic of antibiotic resistant diseases, not to mention the very antibiotics they depend on becoming obsolete due to that resistance; they are facing no longer having any option to do otherwise than breed for resistance, and if they don't start now they are going to lose their valuable genetic stock and have to start from scratch. That'd be a crippling blow for the industry. But they know that, they're aware of what they're facing and are scrambling to find ways to survive it. There's some fascinating research into organic methods going on, lots of testing and studies finally getting some serious funding and interest, and dare I say it, legitimacy. For too long it's been derided and ignored at the expense of total health.
It's still pretty quiet, but many commercial Australian poultry farms and breeders are already altering their keeping and breeding programs to achieve resistance rather than rely on artificial aids, shifting to organic practices and even free range farms etc, on a huge scale. It's only a matter of time before the rest of the breeders/growers are forced to follow suit, it seems. Looks like tumultuous times ahead, for everyone, and possibly some mass outbreaks involved.
I'm not sure it wouldn't be better for them to scrap purebreeding as a rule, only keeping it for some lines (i.e. cell breeding or staggered breeding programs) and bring in mongrels from outside which already have great resistance. Chances are they will have to do so, sooner or later.
I've always selected for productivity, temperament, and all the other desired traits at the same time, with greater importance placed on temperament, conformation and hardiness than most other traits. But I'm aware of how much easier my project has been by virtue of the fact that I've started with mongrels who contain many great genetic lines which have been often terribly neglected on various disease-riddled farms, until only the hardiest survived to breed. Who knows how many generations of disease resistance breeding they've got in them, lol!
I'm in a mild dilemma myself, because we've got pets, which makes things a bit more complicated, both in terms of breeding projects, and my decisions to risk lives to gain flock immunity to a new disease. Some of these pets are old, others 'special' i.e. survivors of injury or illness; almost none of them, however, would have been kept if they hadn't made pets of themselves. While I comprehend and respect the logic of not babying the weak I also value them as sources of greater education than culling the weak ever will be.
I've learned a heck of a lot from trying to save the ill or injured as compared to those who only ever treat illness or injury with an axe, and animal rehabilitation has always been a passion of mine, with a great success ratio, which of course only compels me to greater efforts lol... But beyond a certain point I'm not going to be willing to keep certain animals on the front line as it were.
Currently I'm planning to have several free range but separated flocks, to work on a few projects concurrently, and one of those flocks I expect is going to be a 'retirement flock' --- basically just a safer place where animals with no need to justify their continued feed/care expenditure can continue to live out their days. A pet flock, I guess you could call it. I would take greater steps to protect them from disease, but not to the point of attempting complete biosecurity, and not vaccinating them. That said I certainly don't disagree with anyone else's decision to vaccinate a pet.
Best wishes.