I don't know, a joint project between Mistwalker and Square-Enix would probably be good publicity for both companies. The game would probably do well on just the brand recognition alone, so from a business standpoint I can't see why this couldn't happen since SE and Mistwalker have collaborated with other companies on joint projects before. It really comes down to whether Sakaguchi has mellowed out from his banishment in the early 2000s and if SE still has members of their board members who are still holding a grudge. Considering Sakaguchi has mellowed out on his stance with Sony in the last few years and most of the interviews with old staff from SE show they all still like the Guch, at this point it really comes down to silly company politics and whether the people involved have time in their schedules to do anything.

Who knows, maybe this wouldn't even be a new game, it's possible from some of the stuff they were talking about that the project could very well be a FFVI Remake since the article mentions how both Uematsu and Sakaguchi wish they could have done a more for the game. Whether any this comes to pass is anyone's guess but SE is trying to be more open and change their image among their fans, a game reuniting with the series creator could be a nice PR stunt even if the game never surfaced.