As for Hurt's character being some kind of personal "FU" to Eccleston, bear in mind Moffat claims he's had a plan for "The Fields of Trenzalore/the Fall of the Eleventh" for years now. If the latest post from whistleblower is to be believed,
Which was shot months before the special. Which means his character was created and written well before Eccleston decided whether he was gonna be in the special or not.
Not necessarily. Moffat says in the latest DWM
that they just finished filming "The Name of the Doctor." Assuming that wasn't written in December, then he's referring to more recent filming, such as a day during the Anniversary Special filming.
is shot more like a film than a television series. Jenna-Louise Coleman recently revealed that her TARDIS scenes were shot months after she filmed other scenes from the same episodes. (Probably because the set was still being constructed.)
My guess, assuming Whistleblower is correct, is that Moffat originally planned for Eccleston to be the surprise cliffhanger in "The Name of the Doctor," but due to Eccleston's decision not to return, it's now going to be Hurt instead.