Yeah but it would still be impossible to allow Al Quaeda to become a recognized state, any nation that would open up diplomatic relations to them would be automatically shunned by the world community (Al Quaeda being the real world analogy to Hydra).
Of course stranger things have happened in comics but they are mostly small time, personal changes such as former enemies becoming members of the main group (Emma Frost for example) but accepting Hydra as a government is too far out to make any sense in any show, movie or comic and i doubt the audience would follow in that direction, not when Marvel is trying very hard to get some realism and believability into their movies while toning down the more ridiculous and out there elements of the comics (which work there).
it'd be complicated (probably involving other major world leaders as part of Hydra), but possible.
A lot of people's origins can be "changed", perspective-wise. America's expansion is considered by some done through purposeful genocide of Native Americans...yet we're not as reviled by many as Nazis.
People don't hate Russians the same way as Nazis, despite Stalin's killings.
Hydra LEFT the NAZI's, so they could , in a sense justify by saying they slowed down the Nazi expansion. And did they have concentration camps and do a Holocaust? The Jewish people made sure we never forget -- maybe no group that Hydra attacked had such organization & dedication?
We'll see how it plays out...i predict a resurrected SHIELD by 3rd season...albeit less funded, and less comprehensive.