Presumably you're a Darwinist, no? I know atheists like to separate evolution from social Darwinism, but if you believe that only the fittest within a species survive, then how can you simultaneously question what happened in terms of aboriginals being displaced by those with more advanced armies? This has happened thruout history, on every inhabited continent, and in every age and era.
Christianity doesn't promote the idea of conquering other nations or people. That idea existed long before the last 2000 years.