This is what I'm thinking; she must have done something drastic for that emotional result, and it seems very odd to have this season go on for as many episodes as it has without one of the core characters present. Him appearing now would almost seem irrelivant, and thus I can only assume that he's been (or will be) killed off.
That said, we're dealing with time travel, Mack shouldn't exist (at least as he does; different upbringing and all), Deek hasn't been born yet, and due to other timeline interferences, characters that should've died didn't, and other characters have led different lives, so who's to say Fitz couldn't be saved from a previous point in time before his death.
Ultimately, all things considered, unless they lose the time drive and Gemma can't remember how to make another one, there's no reason any of the current cast should die. Heck, you can even bring back dead characters or change fates if you wanted.