I just rewatched "Urgo" and as I had just read this story, which I just love and thinks it such a hot edition for that episode, I couldn't help but notice a few things....

Before the happenings in your story:
Sitting very close to Jack on that bed, Sam indeed looks very "hot and bothered" (if you get my drift), with her face shining from a light sheen of sweat and looking a tad ill-at-ease. As if her body's already is reacting to something, namely her proximity to Jack. Not to mention, the look she briefly shares with him.

After the happening in your story:
Sitting close together with Jack, Sam definitely looks much better and more at-ease sitting next to him. Plus there is the finger, that Jack briefly let linger on the back of her hand, with Hammond right there, as she has proposed some solution.

And as if they'd resolved something themselves too, in the space between the infirmary scene and to the briefing room scene.