As EW has noted, the description for the November 19th episode of SHIELD makes it clear that it will be directly following what occurs in Thor: The Dark World. The network description reads, “In the aftermath of the events chronicled in the feature film Marvel’s Thor: The Dark World, Coulson and the Agents of S.H.I.E.L.D. pick up the pieces–one of which threatens to destroy a member of the team.”
The November 19th episode, called “The Well,” is written by Monica Owusu-Breen (Lost, Fringe) and directed by Star Trek: The Next Generations’s Jonathan Frakes. “The Well” will be airing less than two weeks after the November 8th opening of Thor: The Dark World in the US, but clearly, Marvel and ABC assume the core Marvel fans will have seen the movie by then.
This is what fans have wanted and we can only assume the same will be done near the premiere of Captain America: The Winter Soldier.