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?