Marvel is already seeking a new director, and as the film is scheduled to be released as early as November 15th, 2013, an announcement as to who will pick up Thor's hammer is expected soon.
There seems to be no bad blood between Patty Jenkins, best known for directing Monster and The Killing: Pilot, and the Studio. It's believed that she may still direct a superhero film for Marvel, but it will not be a sequel.
We'll be sure to keep you updated as to who is hired to helm Thor 2. It's unlikely that Kenneth Branagh, who brought the original in with a worldwide box office take of $448 million, will be back for the sequel. But that hasn't been completely ruled out at this point.