There is no humor in this situation, ever, for either of them, given the circumstances surrounding the death of the little girl. Scully's not making a joke, not one that was meant to make him laugh. We know she's angry because as she see it, she's now been doubly betrayed. The "one true thing" in her life was her trust in Mulder and she's lost that. She's being deliberately sarcastic, even bitterly ironic; that's how I interpret her tone. "Congratulations, Mulder," translating to f__k you, Mulder. He's not laughing. He's shocked. He's flabbergasted. That was the reaction she wanted.

Mulder has a goofy sense of humor but Emily is a deadly serious topic for both of them. He'd never joke about her, anymore than Scully would, that's what I was trying (and clearly failing) to say.