I assume that, as far as battery raised chickens go, they figure they can isolate the new chicks from any wild migratory birds after the buildings have been declared clean. Unlike schools you can't exactly send sick and dying chickens home until the chicken coop is declared uninfected. I suspect they are doing a bit of overkill because the strain spread farther than they initially expected and so quickly. The reasoning probably is to get rid of all the risk they possibly can and start once again in uninfected premises.

Although the initial infection was believed to be from wild birds, the rapid spread to other farms was considered to have been by human means, ie machinery, workers etc. so they are going to have to be a bit more scrupulous in that regard, in the future. Although the virus seems relatively benign in wild birds, ( the mortality rate is low) it would seem to mutate to more virulent strains once it gets into the crowded conditions of domestic poultry.

So heartbreaking, aside from the economic repercussions. I imagine, if the goverment announced that all my perfectly healthy, beautiful pigeons that I raised as a kid, had to be destroyed, I would have been devastated. Its not just large comercial operations where chickens, turkeys and ducks are being slaughtered, but small backyard stuff regarding other bird species as well.