I see the love in the early parts of the story as being implicit rather than explicit. They never say it - well, Mulder does - but I think by knowing Scully's character we can infer the same. She's scared of giving herself completely to another person on an emotional level, but she still stays with him. I think she's doing the best she knows how right now, and trusting Mulder to let her lash out.

I agree. I think this is a Scully who's had all her options taken away from her and has found herself powerless against the machine that's driving them. She's always been the one, of the two of them, who takes things personally, who takes everything to heart. Mulder, by comparison, is a big dog continually following the scent, more open and softer and able to express himself without breaking apart.

I think Scully has nowhere else to direct her anger and sadness, and so Mulder cops the brunt of it, because, as you said, he'll take it. There is literally no-one else she can rail against.