Hi Heather.
In short, I think you know what the issues are. If you use a bad vaccine, you're just breeding a stronger disease.
The real issue, I think, is that if you buy livestock prone to disease, they and their offspring will remain prone to that disease.
If you buy a mess of chickens, vaccinate nobody, and cull or otherwise don't breed any who get sick, the remainder are those with a natural immunity, or who are otherwise unpredisposed to get it.
These are the genetics you want. The only way to get there is to not interfere with the natural selection process, except to speed it up for the sake of easing suffering and financial outlay.
So you choose as best you can, so that your flock starts out as healthy as possible, and from there, you do nothing but separate the healthy ones from the ones who either get sick, or otherwise are outperformed in health and vitality. If they're just sickly, as in weak specimens, they will still make soup, stock, or omnivore
feed. Some cautious sterilisation and cooking of non-infectious carcasses will render them useful, at least for
composting.
And over time, the healthy ones breed with other healthy ones, and you keep removing weak and sickly ones, and your flock, over time, spread the immunity or natural resistance to disease that caused their
chicken forebears to not be culled that first culling.
For me, the livestock vaccine quandary is this: if you vaccinate animals that otherwise would sicken and die, and breed those animals, you pass on their weakness; you end up breeding strains that require the vaccine to live.
That seems dumb to me, or at least short-sighted enough to make me ask if it's a permaculturally-aligned approach. Oh, certainly, treating one animal, one time, to alleviate its suffering and allow it to continue to live and work (but not breed) is understandable. But prophylactic vaccination of unfit livestock so they can live in poor conditions is why the majority of us deplore factory farm conditions and CAFOs. Why does it seem reasonable to extend their ideology even this far?
My advice in short: get strong birds that are unlikely to get sick. If you can get them locally, from a small-scale farmer or homesteader whose poultry you can meet, who also refuses to rely on vaccines, at least prophylactically, then that's your best starting point. If you're keeping everything to healthy bird spec, you might not even need to worry about vaccines.
And if so, remember that compassion is important, but saving an inferior individual does your breeding program no favours down the line.
But do keep posting, and good luck. It would be great to hear how you make out.
-CK
A human being should be able to change a diaper, plan an invasion, butcher a hog, conn a ship, design a building, write a sonnet, balance accounts, build a wall, set a bone, comfort the dying, take orders, give orders, cooperate, act alone, solve equations, analyze a new problem, pitch manure, program a computer, cook a tasty meal, fight efficiently, die gallantly. Specialization is for insects.
-Robert A. Heinlein