The evil vs good theme, in my opinion, is how the OTHER RACES VIEW YOU.
I agree with the above stance. In addition, Good, Evil, all that stuff is, in my opinion, subjective. The main idea for any given culture, though, is that good has the good of others in mind, while evil puts own needs before others'.
If I genuinely believe I do a son a favour by cutting out his tongue when he's talking too much, this is not an evil act by my own standards. However, in most cultures, this would be seen as evil. It's all a matter of perspective.
Personally, I appreciate the little texts that Stardock provided. I find it makes each of the three choices defensible or at least understandable in some way. "I told you before, people are a
renewable resource!" Got a point there. I would find it much less appealing if choices were more along the lines of:
"Starship bonus: Good (0%), Neutral (5%), Evil (11%). Please input choice."
You may or may not agree with what is defined as Good & Evil in the game. Don't take it personally. You may simply be open-minded or philosophical.