I really can't see him going down the road of a REAL Ninth Doctor (I'm not spoiler-coding guesses in a thread full of guesses) because regardless of what has gone on behind the scenes there is no upside to such a mean-spirited reveal.
Making Hurt the "real" Ninth Doctor would not negate Eccleston at all. It would just mean Eccleston would acutally be the Tenth Doctor, Tennant the Eleventh and Smith the Twelfth.
It'd be one hell of a mindfuck, and with implications that would split fandom to epic degrees. But it's not really insulting to Eccleston or anyone.
Now the idea that Hurt's character is meant to be some sort of meta commentary on Eccleston does sound unnecesarily mean-spirited, but there's no reason to believe that at the moment.