I don’t agree with everything you’ve written here, but what comes to mind after reading your piece is that people need to realise a game is something virtual meaning that everything you do in it does not mean you would do it in real life. I feel sorry for people who can’t tell worlds apart, but they should not play video games.
Letting the player choose between good and bad is the essence of a role-playing game (and in many games). RPGs are about what would someone do if he/she were in such terrible world and given only few options to choose from.
And lastly it is not like The Witcher was only about one thing, like any other medium, it has several levels of interpretation, so anyone should be intelligent enough to understand the full length of what the game wants you to play. Like you said, you cannot talk about the lack of other than white skin humans while the game depicts the racial tension between elves, dwarves and humans when you see it as a whole.
That said, I wish our world was more balanced so we could see developers explore more frequently other themes (like cultural references from the African continent or more games from women and their own perception of what a female should look like for example).
In any case, I really enjoyed reading your article. Thanks!