That's the essence of Pinker's point-- the more aware we become of each individual death, the less violent we become, but the more violent we feel. Violent video games are probably the pinnacle of expression of that: our culture is so safe and so risk averse that we become upset by 100% fictional violence which hurts literally no one.
And I feel the comparison between murder and rape is pretty much invalid, for the reason you state. We do have a very serious rape problem, and again, it is obviously not because of all the rape video games out there, or glorification of rape in our culture. It's because real men do not learn to respect real women in the real world.
Again, that's what we should be talking about.