Hi, me here. I never did understand Scully's anger entirely, but I would say it has to do with frustration. Maybe just simple sexual frustration. Maybe the sadness of knowing that a normal New Year's Eve date is something they'll never have. She just kind of loses it. People do, even Agent Doctor S. But the story itself is a little too complicated for me. I'm not sure it ever can be fully explicated, which is a cowardly way of saying you're both right. This is one way collapsar goes, between these two. Incidentally, so far as canon is concerned, I remember the selling of the "New Year's kiss" and the fever of the fans. I think that bloodless little smooch was Chris Carter's typical way of reducing the ship to a tease rather than a complex and acknowledged reality. It was his curse, that ship, and he went down with it. But people like Khyber--is there anyone like Khyber?--gave it the importance the actors at the very least deserved.
Re: 1. Collapsar