I don’t think it’s compromised at all. Indeed, I would argue that the Cold War propaganda is important historical material to be studied, to look at how pop culture reflected the politics of the day.
But I woudln’t argue that “ no attempt is made to complicate the alliances the heroes have with US Foreign Policy.” Marvel in the late 60s onwards is very very different from Marvel of 1961, and that includes foreign policy.
As for Doctor Doom, I don’t think he’s U.S-backed. My understanding is that Latveria was firmly non-aligned, like Namor’s Atlantis, T’challa’s Wakanda, etc. Man, the Marvel Universe version of the 1961 Belgrade Conference must have a hell of an event.
And I believe Captain America has indeed mentioned that – sometime in the Rucka run, if not before. Hell, Cap did fight on the Eastern Front for a bit, so he knows it first hand.