He doesn't assume it's comfort for him, only that she's still overwhelmed by the news. You'll live, but you'll lose everything - but some of it, you won't regret. It's nothing he can say to her right now. He hugs her back, pressing a kiss to her head. "It's okay."

Mulder pats her back, trying to think of something, anything, that'd be a comfort. When she's no longer clinging to him - no longer sobbing, just hugging him tight - maybe he'll get the picture out of his wallet. She deserves to see his face.