Here is the word from Comic Book Resources:
"We all love Clark Gregg, there's no doubt about that," Whedon said. "From before we made 'The Avengers,' we discussed whether there was a way for him to be a part of the Marvel Universe, perhaps a part of a TV show even after his death. … The fact of the matter is, as much as we love him, now that I'm really running Marvel, I like to keep a type of artistic integrity, which means we don't stretch the bounds of reality."
"There was never going to be a 'S.H.I.E.L.D.' show without Agent Phil Coulson!" said Feige, who appeared behind Whedon, wearing a COULSON LIVES shirt.
"He's headlining the S.H.I.E.L.D. show and always was." said Whedon.