You know what? Scully spent the whole episode (and season) having a mental connection with William. I think she knew damn well he wasn't dead in the end. She was just shocked and trying to ease the blow on Mulder about William not being his son by trying to disconnect herself from the whole broken motherhood experience... While also trying to tell him what she clearly had been wanting to tell him throughout the entire episode. I rewatched it and she sees to always be on the verge to want to tel him something.
That's the only way I can fathom her reaction / lines / attitude after knowing William fell in that water














