ocpmovie said that you might be able to get someone to add some cuts and whathaveyou to Neo's face to accomplish what you are hoping. In that same vein, you could also grab clips from the movie Sweet Nomber with Keanu Reeves and Charlize Theron. There are a few scenes that have him wearing a blind-fold and wlaking around. My idea is that you could rotoscope his head out, or his entire body and plug it into the few scenes where you see that he is in fact alive, albeit blind or healing (either could be suggested by the covering over his eyes).

I realize that this would be difficult and perhaps more work than you want to spend on something, or it maybe too far from the direction you want to go with Neo's survival, but it's just another way you could possibly make it work. Oh, and I am totally supportive of any and all edits of the Matrix trilogy. I would hope that you would leave the original alone mostly since it was great IMO. However the other two, especially Reloaded, really needs an overhaul.

One last thing, as long as we are on the topic of rotoscoping, at the end of the Matrix (the first movie), he looks at the agents down the hallway and sees them in Matrix code. The problem is that they are green and in code unlike other programs in the Matrix. In Reloaded and Revolutions all programs are orange. Even when Neo sees Agent Smith during their fight on the ship seeing him extranaturally(?) he sees him in orange almost as if he were on fire. Seeing as the creators of the Matrix decided to change the look of programs for the sequels, I would like to see the agents at the end of the Matrix as a deep brown almost black silouhette with an orange outline like how the programs are represented in the sequels.

Just some thoughts.