For a commercial flock that will never be used for breeding anyway, if almost all of the birds would die from the disease, I think it can make sense to cull the whole flock. It saves human time & effort (do it all at once and get it over with), and depending on what method of culling is used, it may also reduce suffering among the chickens, and it does prevent disease being spread from those particular chickens to wild birds or other flocks.
But for breeding flocks, I think it would make more sense to allow the disease to run its course, and breed from any survivors. For breeding flocks that belong to hatcheries, where the chicks will be distributed to people all over the country, I think it makes even more sense to allow any surviving chickens to breed: talk about a good way to spread genes for resistance! I think some sort of quarantine would make more sense for such flocks, to prevent any extra spread of the disease while it runs its course.
Which is to say, I don't think any "one size fits all" approach is correct, but of course the people writing government policies didn't ask my opinion (or apparently the opinion of anyone else here!)