It could be done very well - a "Tomato in the Mirror" surprise that the best Final Fantasy games did so well, where the main character hasn't realized his entire history is fake. Cole had that story arc in the novel Asunder, and it really worked.
It'd be useful from a gameplay stance, too. It would explain the lack of a playable origin, and give them the perfect excuse not to include the main character in future games.
That said, I don't think the fandom would react well to it, and not just the ones in this thread. Dragon Age fans are a conservative lot who keep demanding that the devs remake old games, and who get so attached to their characters that they keep demanding the Warden back. Most major plot twists post-Origins get very poorly received. I'm trying to imagine players suddenly discovering after 120+ hours that their backstory was a fake.
(A small quibble is that humans don't seem to become spirits - although that possibility is left open. The divine was most likely a spirit imitating her. Of course, in some playthroughs, there is another spirit masquerading as a human
So this has happened more than once.)