You know, I'd argue that, if you were a random stranger who had no previous experience with either game, you'd be more likely to have your heartstrings pulled by the Call of Duty 4 cutscene. Seeing the aftermath of a nuclear strike, watching your belief of invincibility (hey, I'm a player character, I can't die!) crumble around you, and the shock from it, that's pretty damn powerful. It's also a whole lot more effective in expressing 'Nukes are bad' message, what with you witnessing the destructive power o a nuclear weapon, first-hand.
That said, I'd still take the World in Conflict nuke scene. Why? Bannon, while being presented as an arse from the beginning till the time of his demise, becomes a sort of redeemed character after you learn of why he was such a "god damn cowboy". If you didn't feel anything in that cinematic where Bannon's mother is listening to her son's recording on the answering machine, well...