He wouldn't have to accept Disney's input. They don't take over control of the film franchise until after The Avengers. Until then, Paramount still has controlling interest.
I probably should elaborate...
Disney though their partnerships with Sony and MGM have had control of every single Marvel comic based movie to come out since the fist X-Men in 2000. They started actively taking over the company (buying open shares) in 2006 and formerly announced their intentions in 2009.
I have a short list of how Disney has influenced the X-Men movies they have influenced more than just the X-men movies and this is just a small sample of what they have done.
The Anna Paquin descision in having her cast as Rogue not be able to fly or have her at any point ever encounter Ms. Marvel came from Disney.
Shawn Ashmore cast as Iceman and being a teen instead of one of the Original X-men came from Disney.
Aaron Stanford case as Pyro and being a teen instead an original member of the Brotherhood came from Disney.
Steve Bacic cameo in X-Men 2 as Hank McCoy came from Disney.
Daniel Cudmore being uncredited for his role as Colossus in X-men 2 came from Disney, he was almost removed from the movie entirely because of the POSITIVE responce that a test group gave the pre-screening.
Nightcrawler not appearing in X-Men 3 came from Disney.
The change in casting of Kitty Pryde from Katie Stuart to Ellen Page in X-Men 3 came from Disney.
Fox Studios Fired Bryan Singer despite Disney's protest to keep him on for X-men 3.
Nightcrawler's appearance in X-men: First Class came from Disney.
Disney decided to bring back the gay activist director/story writer Bryan Singer for Xmen: Fist Class due to his unpopular alternate story line that almost killed the franchise. They did not give him any special instructions to keep his activism out of the movie, unlike he was given by DC comics when he got picked up to direct the Superman movie.