When I recently re-played Deus Ex (Human revolution), you can choose to play the game in a pretty much pacifist way. I didn't do that, but at the same time I didn't go laying a trail of carnage through the city, killing the police, etc.
The game puts you in situations where you usually have a choice about your actions -- I can sneak around (harder), I can kill the guard, I can kill the police officer, etc. I had no problem killing the mercenaries that would shoot me if they saw me, but after killing an NPC police officer (in frustration after setting off alarms), I felt compelled to do it again until I could master doing nonlethal takedowns, or knock them out with a sedative dart.
I don't think this is a matter of having a problem separating fantasy and reality. Rather, it's a lens to look at our own behavior and feelings about violence. I have no problem shooting other players in the face in a game like Call of Duty or Counter-Strike (which is effectively paintball), but I get deeply disturbed at the idea of killing (or spawning + harvesting?) non-hostile NPCs in games like Minecraft or Deus Ex.
Games with that degree of role-playing are fairly rare to begin with, and most people also don't get terribly immersed in them, so often that NPC you care about to them is just a number.
I generally treat everything in Minecraft very mechanically, as numbers, because Minecraft just feels that way to me. But in a proper RPG, it's not so simple.
Most people would not enjoy child rape simulator 3000 because most people do not have embedded instincts to do such things. Some people, however, may enjoy CR3000, and I would venture to guess that there is an underlying reason (i.e. pedophilia).
Being used to see violence in fantasy doesn't make you violent deep inside, you just don't give it that much importance in fantasy. This doesn't mean that you won't despise real violent acts.