That the executive branch in the late '40s and 1950s was "full of treasonous pro-Soviet intellectuals", in Arthur Miller's phrase, was very much doubted. He, of course, was the author of "The Crucible" which is a depiction of the Salem witch trials and was an explicit allegory of McCarthyism as a witch hunt. At least that's what I was taught growing up.
The distinguishing attribute of a witch hunt is that the thing being hunted does not exist. It's like a snipe hunt. The message of The Crucible, at least the way I was taught it, wasn't that the wrong people were accused of the witchery going down. It was that the entire hunt was fraudulent and paranoid, because witches aren't real. Or in the common vernacular, "there's a red under my bed and there's a little yellow man in my head". The "Red Scare". Again, suggestive of paranoia.
So, I was raised doubting exactly the things you suggest cannot be doubted, and I don't think those doubts were uncommon at all. Venona makes those doubts look ridiculous. Although people are still calling it a witch hunt, and people are still making excuses for the Rosenbergs.
McCarthy was famously ineffective and incompetent in doing anything about the very much non-witch Communists in government who committed treason to further the cause of a communist dictatorship in the US. Who did a better job than he did in hunting them down while they could still be punished for their crimes?
Who did a better job than McCarthy? Quite a few people who did not get any headlines, persons serving in the FBI or in executive departments' security arms.
And I think that one should distinguish between persons who once joined the CPUSA, then later thought better of it, and persons actually engaged in espionage. The US engaged in a certain amount of ritual humiliation of these people, and so won them a degree of sympathy entirely out of proportion to their judgment or character.
We know from Venona the names of dozens of spies for Stalin in government during this time period. What percentage went to jail due to the efforts of, "persons serving in the FBI or in executive departments' security arms"?
> I think that one should distinguish between persons who once joined the CPUSA, then later thought better of it, and persons actually engaged in espionage
This is true, there is a difference between treason on the one hand, and joining an organization that advocates treason on the other. One carries a death sentence, the other is protected under the US Constitution.