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First, your barnyard birds are genetically different from their wild cousins. Wild chickens either have a natural resistance to internal parasites that maintains an equilibrium or they die and hopefully don't pass susceptibility on to their offspring. This is a natural consequence of the difference between Natural Selection and Husbandry--humans select for traits that might not survive in the wild, because management makes it possible to retain desirable traits that might not contribute to overall success in the wild.
Note also that 'natural' does not mean either 'safe' or 'organic'. There are plenty of natural things that your chickens could get into that might well kill both worms and the host. You have to also do research for every species you work with, because different plants can either be benign, effective against a given threat, or deadly poisonous for the animal. Stuff I can give to sheep, I'd never give to a Llama, or could disrupt a pregnancy, and the Gods can only guess what it might do in a chicken, or whether eating the eggs is advisable.
I think this is wonderfully stated. Barnyard birds are bred primarily for productivity, with some consideration for hardiness but not much. And there are tons of studies on parasites. It's very important to understand exactly what parasites do and how they work to truely understand which products will work and why.
I am a huge fan of natural stuff and its use - but being a huge fan, I find it's my responsibility to also know when to strip products of their super-product cape and just like them for what they can do, not expect them to do what they cannot. I've been using DE in my flock for over a decade and I've found that it is simply not a dewormer. Yes, it can help reduce populations, but it will not treat infestations. I wish it would, but it won't.
Rather than throwing the proverbial baby out with the bathwater, use the natural products for what they're useful, and then realize when it's time to use something stronger. Talking about immune systems and the design of the body, birds who are infested with worms wouldn't purge - they'd simply die. If poultry were so savvy, they wouldn't spend all their time eating all the intermediate hosts of the parasites.