I haven't played Black Ops 2 or CoD 3, but in the eight other CoD campaigns that I have played I can only think of two occasions where enemies were taken prisoner and not killed. (some Jerries surrender to Price in CoD2, and some terrorists in MW3 are apprehended in the London tube if you choose not to shoot them in the back as they flee) Now I don't expect a CIA assassin or ruthless Soviet conscript to offer quarter, a zealous Taliban or Imperial Japanese soldier to ask for it, but in some cases I wish the last few baddies of a slaughtered battalion would just give up. But as it is, even downed, wounded soldiers will draw a pistol without fail and force your hand.
But for the most part, I think egregious violations of 'the rules' (Price beats then executes a captured, bound villain in MW1) are not portrayed in a way that can be mistaken as 'okay' unless the player totally misses the point.