No, they're just suggesting that - a lot of these videogames are pushing the realism factor, especially military shooters. And that if you're striving for a realistic depiction of war, then a realistic depiction of the rules of war and engagement would probably be a good thing to add alongside that. I don't believe anyone is saying that you, as a player, should be punished for your actions in-game.
Also keep in mind that the Red Cross is hardly going to be the most gaming-savvy organization out there. I kind of like that they're not suggesting specific mechanics or game design paradigms that they likely have little knowledge of or background in, and are more kind of throwing out an open suggestion on improvement that they'd like to see in gaming culture.
I don't see anything wrong with placing those actions in proper context, however. I didn't see anything in that article that would suggest these guys want to take away any opportunity to allow you to play as a villain. But I do personally feel that if you're going to be having this sort of questionable content in a videogame, that it be given at least some manner of context and weight, and be dealt with in a mature manner.
If you're already playing as an evil military dictator in whatever hypothetical videogame we're talking about here - then being wanted by world authorities to answer for your character's war crimes would be not only appropriate, but could potentially offer more compelling gameplay alongside that.
I suppose it comes down to what you want to read into that article. I'm just not seeing it as a flat statement that "every violent videogame needs to deduct points from a player for acting out of accordance with international law, regardless of context." What I rather got out of it was that, yeah, some acknowledgement that these concepts exist and that your character in whatever game is taking action within those contexts - for better or worse - could make more better games, potentially.