This isn't about the movie of this post, but I want to expand on something:

"it's a movie where Nazis take over a flying aircraft carrier"

WARNING: WINTER SOLDIER SPOILERS TO FOLLOW

No it wasn't about Nazis taking over. And I'm not just talking about the distinction between Hydra and the Nazis, and how Hydra had it's own separate ambitions, and only used the Nazis.

The subtle point is that an organization can't take in corrupted, moral-less people, give them important research positions, and believe the organization's culture itself wouldn't be affected. Like how BW told Cap about Operation Paperclip, a real-life operation where Nazi scientists were pardoned to work for the CIA. It's about how SHIELD itself, no matter how noble its original intent, became a corrupted organization through bringing in and allowing amoral people to do important work for them, naively or arrogantly believing itself incorruptible.

That's why Cap and the rest were adamant about taking the whole thing down, not just the Hydra operatives. The corrupted influence had spread so ubiquitously throughout the organization's people and culture over the decades that two were not only indistinguishable from each other, but even from their original states. They were effectively a new hybrid entity.

There was no salvaging SHIELD, one could not simply remove Hydra from it. The two had slowly and unknowingly merged over the century. At that point, all that could be done was to tear the whole thing down and maybe, someday, build something new.

At least that's what I took from it. I did initially groan when the movie first starting referencing current day Hydra members. I wish they didn't. They still could have brought Zola and others on board during Operation Paperclip, but if they never had any of them going "hail Hydra" (which by the way a lot of Machiavellian Americans operatives within SHIELD had been doing, showing it wasn't a Nazi thing) then I wouldn't have this point gone missed, and so many comments online going "oh jez, it's the Nazis yet again". But I understand they had to bring the organization back for fan service.