The actual fact is that the chickens hatched from those eggs are individuals. They aren't identical to either of their parents. The differences are small, but small differences can add up over time. It's taken humanity only a few thousand years at most to breed many varieties of chickens; you should tour our State Fair poultry barn sometime during the competition and see just how different chickens can be made to be. Keep the genetic pools separate long enough, and you'll get varieties that can't interbreed--they'll be separate species.
It takes a very long time for most species to diverge, but the time scale isn't years, it's generations. Populations of fruit flies diverge so quickly they become incapable of interbreeding in very short times, and once that happens, those populations are on permanently separate paths of descent.
Human generations take much longer than fruit-fly ones, and considerably longer than chicken ones, so even the populations that existed separately for long enough that they look very different are still able to interbreed (as, for that matter, are the chickens--so far).
As to the deaths of millions, your reference link is bad, but I agree that several very nasty social philosophies have tried to incorporate evolutionary concepts. But these have nothing to do with evolution as science; they are attempts to co-opt it into something unrelated, and entirely unscientific, just because it's trendy. If they hadn't been able to twist the notion of evolution, they'd have used something else, or done without. Neither Nazism nor Communism would be substantially different if the theory of evolution had not been published.
Social Darwinism would be different, but only in name; notions of "fitness to live" measured by prosperity were bandied about long before him. You can find a critical reference to the notion in Dickens' "A Christmas Carol," published 16 years before "The Origin of Species":
"Will you decide what men shall live, what men shall die? It may be, that in the sight of Heaven, you are more worthless and less fit to live than millions like this poor man's child. Oh God! to hear the Insect on the leaf pronouncing on the too much life among his hungry brothers in the dust!"
Ideas don't kill people; people kill people. And people who kill people are usually the ones who care more about assembling arguments than they do about seeking truth. That's why the modern "prosperity gospel" is a greater companion to Social Darwinism than evolution ever was.