I had considered that angle, and I think it's legitimate, of course. And it works as a metaphor, like you said. That is, it sort of works for me. For one thing, it might impel some viewers to compare what our governments and military contractors are doing with some of the behavior of police states, past and present, in this case the Nazis.
I agree that's ballsy. I agree there's something substantive there. I think they're in the right ballpark, at least.
But I'll try to clarify why I still think it's ultimately a cop-out. Ultimately, it's a cop-out because, literally (while, okay, perhaps not metaphorically, as you say), the real bad guys turn out to be not us, but them. Instead, it's Hydra --fictitious Nazis who have infiltrated us and ours. Which, at least on one level, so far as I can see, ultimately pulls the rug out from under that otherwise noteworthy commentary you have described.
From a metaphorical point of view, perhaps that doesn't matter. But from a more literal point of view, it seems to me we have ourselves a scapegoat. Actually, we have a bogeyman who will be our scapegoat. Instead of what could have been unflinching self-criticism and self-analysis, we have an alien force (an imaginary Nazi organization) to place the blame upon.
Contrary to, or in spite of, that point, there is another possible, positive aspect or outcome to the narrative as you see it which interests me. Whether or not my view that it's a cop-out has any merit, there might be something worthwhile that some viewers might take away from it, something, in fact, that the filmmakers may have intended. Even though it turns out to be Hydra who is the real culprit, it may occur to some viewers to consider what would happen if a such regime, something far less benign than the one currently in place, did/does come to power. It will have this military/surveillance apparatus at its disposal. Is that okay?
So hey, I didn't say I didn't like the movie. I only said I was disappointed with that aspect. But I wouldn't want to throw the baby out with the bathwater. I'll take what I can get. So anyway, I pretty much agree. Bravo, Marvel, for doing as much as you did do. With just a little caveat. =P