I also rewatched the scene again, and at the very start there is a long shot from behind where the crew is standing looking at the pod. Since the pod has a big window on the side, you can actually see Fitz stand up through the window (he's easy to distinguish from the others because he's in a light blue shirt and everyone else is in black) and walk towards the door. So since Jemma was in front of the shot looking at that window, she would have seen Fitz. She walked closer to see if there was anyone else there not visible through the window where she was originally standing.

Now, I'll concede that maybe they didn't mean the scene to play that way, maybe she really was just as relieved to see that Fitz was okay. But again, they purposely leave it a bit ambiguous what exactly Jemma feels, and it's not even totally consistent from episode to episode. I mean, last episode, she didn't even want to try to get Will back, and now she's devastated that he didn't come back?