It was probably Kevin Feige, sometime before they finished shooting Avengers.
In an interview with /Film, Kevin Feige (president of Marvel Studios) was asked this question pretty directly. Since Feige sits near the top of the Marvel production food chain, it’s likely he made the decision to run with this idea.
It sounds like this is an idea floating around when they were making First Avenger, and it got locked down shortly after they finished shooting Avengers. Here’s his full answer:
So you spent eight movies and a TV show building up S.H.I.E.L.D. and then in this movie, you say good-bye to S.H.I.E.L.D. When did you get that idea to sort of have HYDRA be underneath it all?
Well it was sort of a notion I had in the back of my head during Captain America 1 when we were sort of plotting the timelines for Cap and Avengers. The S.S.R. and Howard Stark’s involvement and, you know, people always ask, do you have master timelines of all the different movies? And we don’t really, but we do have timelines of the details of some of the movies, like the Stark family and things like that. And we were putting that together. And I started to get excited again, just sort of in the back of my own head about the idea that the S.S.R. help defeat the Nazis obviously, but also HYDRA. And that would make sense that the United States truly did bring in some of those HYDRA scientists and experts in technology to incorporate it and that much of what became S.H.I.E.L.D. signature items were a part of the HYDRA Corps brand. And what if you took that to another level and said “Oh, they’ve been in there the whole time, they’ve been growing in there the whole time.” And at some point reveal that much of the work S.H.I.E.L.D. had done was all for this, for the purpose of eventually bringing back HYDRA.
And I think the first person I actually sort of verbalized it to was Chris Evans. On the last day of shooting we were in Central Park on Avengers and he goes “So what are we doing for the next one?” I said, “Well, you know, we love Brubaker’s Winter Soldier, we think there could be something there. And have Sebastian [Stan] become a totally different version of himself. We also have this notion about SHIELD.” He was like “Holy crap, what the…?” And just based on his reaction it was like, “Oh maybe this is good.”
Since the idea wasn’t decided when they were making First Avenger, there probably weren’t any explicit decisions made which foreshadowed the HYDRA reveal. They may have made decisions that would make such a plotline easier to justify later (or at least not ruling it out), but not directly leading to it.