McCarthyism is similar to a witch-hunt, but it's not the exact same thing. A witch-hunt is the hysterical search for something that does not actually exist. McCarthyism refers to the making of unfair allegations without due process or legitimate investigative techniques. The fact that an unfair or random allegation may turn out to be true does not legitimize the justify the technique or removal of due process. Both techniques involve terrorizing innocent citizens.
Were someone to go into a ghetto and slay all the black males between the ages of 14 and 21, they would certainly kill a few criminals along the way. That doesn't make it any less unfair to all the innocent people who are not committing crimes.
Also, the First Amendment clearly makes it perfectly acceptable to hold and express alternative politcal and economic opinions from the ruling class. McCarthy not only (randomly) targeted government employees, he also went after film makers, writers, teachers, and other American citizens.
A small number of the hundreds arrested or tens of thousands who lost their jobs may have actually had Communist sympathies, the vast majority of those terrorized by McCarthy had done nothing wrong. Simply being accused was usually all it took to lose your job and be added to a no-fly^H^H^H^H^H^Hblacklist.