I've been thinking about this since I saw Captain America: The Winter Soldier. It does hinge on that big reveal, so maybe this is a spoiler for the movie, or the Agents of SHIELD series, if you were waiting to catch up on that.
So, you know, look away if that's an issue.
OK, there's the reveal that HYDRA's been lurking within SHIELD for decades, using it to carry out their schemes. What I was thinking about was, how does this affect that Agent Carter TV series we're supposed to be getting? The whole HYDRA thing kind of casts a pall over the missions she takes, because we're going to be wondering if she's unwittingly carrying out HYDRA's goals. You can obviously have her get suspicious, start trying to ferret out the truth, or maybe figure out ways to not carry out the objectives in ways that won't get her fired. But the fact HYDRA persisted all the way up to the point Steve Rogers finds Zola's brain recordings in that bunker would imply she ultimately failed. Which is kind of depressing. Or she stopped trying, which doesn't seem much like Peggy Carter.
I'm not trying to be a downer before the series has even gotten started. I think it could be very cool, and I hope it is (though I haven't really heard good things about Agents of SHIELD, for what that's worth). It's possible they could start out with things going well, then gradually turning more sinister. Carter notices the shift, starts trying to trace the cause, runs into stonewalling or missions that seem like they're meant to get her killed, and the end game would be she deals HYDRA a crippling blow, but a few of them keep their heads down and are able to start over. Cut off one head, two more, etc.
She's going to be working for SHIELD in its very earliest stages, so perhaps they can argue HYDRA hadn't started twisting things around yet. Problem there being, I can't imagine SHIELD or the OSI waited long to recruit Zola. Like they just left him sitting around in Switzerland, twiddling his thumbs after Cap went into the drink.