I don't see any reason they wouldn't be able to fix this. What I'm really hoping is that we can have both a live Hero of Ferelden and an Orlesian Warden. There's no logical reason that it couldn't happen that way - I had a Dwarf dwarf who became a Paragon and went straight back to Orazammar after the Blight, and another who took off looking for Morrigan. Neither of them were in Amaranthine to handle the events of Awakening, but they're both still alive. (Or they were at the end of Witch Hunt, anyway.)
At the very least, though, I'm expecting to be able to record the decisions of the Orlesians who took over for my two ultimate sacrifices.
The idea of a living Warden not being at Amarathine throws a few weird little ticks into the mix. Let's look at some possibilities:
Option 1:
Origins: Ferelden Warden. Lives through the final battle, elects to remain with the Wardens.
Awakening/Golems/Witch Hunt: Continues adventure of Ferelden Warden.
Option 2:
Origins: Ferelden Warden. Does Ultimate Sacrifice (or elects to leave the Wardens)
Awakening/Golems/Witch Hunt: New Orlesian Warden.
Option 3:
Origins: Ferelden Warden. Lives through the final battle, elects to hunt down Morrigan.
Awakening/Golems: New Orlesian Warden.
Witch Hunt: Return of Ferelden Warden.