I've always been able to do a Save & Exit and get Return To Base.
IIRC if you try to exit the patrol while submerged it tells you that you can't return to base while submerged, and then you either have to continue or else abandon the mission/career you're playing. Otherwise I can't remember being given only the options of Continue or Abandon when my boat's still good and I haven't already been KIA.
After you hit Esc, are you choosing Exit or Save & Exit? It's possible, I guess, that if you don't hit Save & Exit, the game thinks you are abandoning the career because you're not saving at that point. The game does an autosave at the beginning and end of every patrol, and I'm not sure it matters how the patrol ends. Might be why there's a save there that says you're dead, if the game equates Abandon Career with KIA and autosaves at the end of the patrol where you "died."