There's a very important scene Spielberg included in Saving Private Ryan where our heroes murder surrendering Czech soldiers in cold blood and then laugh about it. This is one of the less glamorous elements of D-Day in particular. A fair number of the people the Americans and their allies killed a Normandy were not Nazis. They weren't even Germans. They were conscripts from captured territories.
I think it's very dangerous to start glossing over the unpleasant realities of World War 2 in order to convince ourselves were were the super duper good guys and "The only good Nazi is a dead Nazi" is anything other than a destructive insanity that will eventually result in you lining up civilians and shooting them because, you know, they were probably Nazis. There's that very bleak sequence in Call of Duty: World At War where Reznov instructs you to kill unarmed Germans. You can either shoot them or burn them alive. It's a very unpleasant scene. Reznov is blinded by pure hatred for Nazis. It doesn't matter whether these people were Nazis. That is where war crimes come from.
Notice that enemies in Wolfenstein never surrender? You have no choice but to kill them or they will relentlessly seek to kill you. If Wolfenstein's enemies got down on their knees and begged for mercy, Perfect Dark-style, I think that would raise certain uncomfortable emotions in the audience that would not play well. The gleeful Nazi killing would suddenly start feeling a little... off. Datadyne in Perfect Dark is a really bad company. Its soldiers are fragile, even through they're responsible for a lot of bad things. "I'm just doing my job," they beg. "Please... don't!" they sob. Sometimes they literally throw their weapons away unprompted and beg to live. Various games have featured similar mechanics over the years. None as elegant as PD, though, IMO.
Killing enemies who only seek to kill you and cannot be halted any other way is inherently justifiable. It plays well, tonally. Killing unarmed enemies in cold blood... that jars the power fantasy. I am pretty confident that enemies never surrendering in Wolfenstein games is a deliberate design trait that serves to make the player feel better about killing.
I'd contrast Wolfenstein and Metro. In Metro: Last Light, you fight neo-Nazis of a kind. Bad, bad people. But you're not forced to kill them. The game is going for a very different tone, probably because Artyom, your character, committed genocide himself, and there's an underyling theme of forgiveness that, to be honest was probably cribbed directly from Ender's Game.
