I think it's different because a neutral run and a no mercy run are different, and a playthrough executing major characters doesn't change the game significantly.

I think the writer (and the player, of course) are supposed to work through those things. It's a very complicated trick to make you love the characters, leave the option for a no mercy run, then shame you for even attempting it.

I agree but it also only came about because it was the title for the first big video that did it, and he named his main character "Hitler", so the creator's a little uncomfortable with holocaust jokes in a game you're supposed to take seriously.