Could it be that he was actually using the whole thing to set up Norman Osborn for a fall?!

I wrote a fic involving that premise this time last year. Tend Towards Decay.

In that fic, Tony apologized for the video message, saying he was in such a low place when he made it he thought they might pull the plug, but in retrospect he knew that was foolish. Thor and Bucky will not let a guy die if they can reasonably prevent it, because they're heroes.

Also, I can well believe that Tony kept the pre-Extremis copy of his brain specifically in case of a catastrophic Extremis failure.