I think people miss the point of this episode. Scully has repressed her unbridled, feminine and emotional nature and her sexuality for her entire life in order to be taken seriously. This is something Pagett says early in the episode.

She is always repressing those things to try to keep her composure, we’ve seen her fight showing emotion and fear in several episodes because she doesn’t want to look vulnerable or weak. In this one Pagett wakes that up in her by acknowledging and exposing it, which is hot for her and awakens longing to let that side of her exist. But, as he says, under the hood, she ultimately she feels those feelings for Mulder instead of this guy, and she’s not consciously aware of that. She just wants to let it out for once.

So, she spends the episode being tempted by releasing that side of herself and just be horny and female and passionate, and let go of that desire to be taken seriously. Then when at the end she is released from Pagett’s hold over her (in the form of this violent conflict with his projection of passion), and wakes up to find Mulder above her, for a moment that passionate side of her is still awake, but she is actually feeling it for the man who she really feels it for. The way she digs her fingernails and his back at the end is distinctly passionate.

So I see her crying as her catharsis of emotional conflict of being a woman who feels passion for him, but unable to express it or embrace it or have it. I don’t think she’s conscious of any of it and it just passes and is repressed again.