The author's problem with the game is, in fact, that it ends up mirroring Nazi ideology almost exactly: Manly men with superior genes and culture, looking for lebensraum, improving the effeminate, "weak" culture they're colonizing. Oops.
I think no religion or religious organization should be spared of critique, but realize that in the West, (Christians), have been exporting culture that's kind of about trashing other peoples.
Take a look at Call Of Duty or even something as innocent looking as Uncharted for how 'we' are treating other cultures.