Well, it now seems as if the media is calling it, and that they think she'll appear in the movie.
“I can’t say yet because it hasn’t been officially released, and Marvel are very protective of their franchise,” Atwell is quoted as saying by Bleeding Cool, Comic Book Movie and others. It's a line similar to what we all heard from Kat Dennings about a month before it was announced she would return for Thor: The Dark World.And while the consensus is that it's a non-confirmation confirmation on the part of the actress.
Still, a non-disclosure agreement might be broad enough to prevent her denying involvement specifically, too, as it might preclude some of the other approaches to the storytelling that the directors have talked about (e.g., having Atwell appear in flashbacks that inform the Winter Soldier portion of the film) or confirm casting rumors regarding the other female actors vying for Cap's attention in the forthcoming film.
There's also quite a bit of speculation that Sharon Carter may be added to the film, something that seems to make sense given the fact that we're talking about the Winter Soldier storyline, something that came during Ed Brubaker's fan-favorite run on Captain America during which Sharon was a major part of the plot.
Still, there's another woman unaccounted for in all of that discussion--Sin, the daughter of the Red Skull, who also plays a fairly key role in some of the later Winter Soldier stories and who may be a more reasonable way to tie the Skull back to potential sequels than to have yet another character who somehow managed to survive to the modern day. In the comics, with such things spaced out over a number of years with a lot of adventures in between, it may not be so distractingly unlikely, but it seems as though it would be more difficult to pull off onscreen.