Could you give a few examples of those worst outrages?

Have in mind that the New Deal and WW2 are at the very heart of the political myth of the modern U.S. (and the whole modern West by extension). Demythologizing this part of history is extremely difficult, since huge inferential distances have to be bridged and much counter-evidence to the mainstream view must be marshalled before it's possible to establish a reasonable discussion with someone who is familiar only with the mainstream view, even assuming maximum open-mindedness and good faith on both sides.

(In fact, one of the reasons for McCarthyists' seemingly obsessive focus on Communist infiltration was that although they perceived correctly at some level that the problem was much deeper, they never dared to proceed with any further serious attack on the whole grand sacred myth of FDR's regime. The Communism issue was a convenient thing to latch onto in their struggle against the New Deal establishment, since it was by itself an extremely powerful argument but didn't require questioning any of the central untouchable sacred legacies. In a way, FDR managed to play the ultimate head-game with all future American right-wingers by wrapping his legacy into the image of a great war leader whom someone strongly patriotic can't despise without feeling disloyal. Sometimes this leads to grimly amusing stories, like when a few years ago American veterans protested over a new WW2 memorial that featured a bust of Stalin along with FDR and Churchill.)

The least controversial examples, however, are those related to the American cooperation with the Soviets during WW2 and in the immediate post-war period, many of which go far beyond any plausible claims of strategic necessity. Some of them are in the "outrage" territory by any reasonable meaning of the term, like for example the Katyn massacre coverup or the Operation Keelhaul. Another example, which was perhaps the principal impetus for McCarthyism in practice, was the handling of the civil war in China (see the OB post I linked elsewhere).

McCarthyism was the belief that unelected officials should be accountable to elected ones. And that that accountability extended to having them fired for having Communist connections. And that this applied not only to unelected government officials, but movie-makers and teachers and union leaders and so forth. And that "having Communist connections" should be interpreted very broadly indeed.

In a sense, you are right. It would be fair to say that the McCarthyists -- again, using the term loosely, not specifically for McCarthy and his personal sympathizers -- did want to make Communism disreputable in a similar way in which racism is nowadays. For a brief while, they had some success -- some people's careers were seriously damaged due to their supposed Communist connections, much like many people's careers are damaged nowadays due to their supposed racist beliefs or connections. And indeed, as always happens when ideological passions are rife, there were some overbroad interpretations of Communist connections and sympathies. (Just like today it's by no means necessary to be a card-carrying neo-Nazi to be accused, with serious consequences, of "racism" and "hate.")

On the other hand, the McCarthyists were by no means the first ones to start with such hardball ideological politics. FDR's regime certainly didn't use any gentler methods to destroy its own ideological opponents, and the tactics that were used against McCarthy and other similar figures of the period were also every bit as dirty from day one. (By the way, did you know that the media assault on him was in fact CIA-orchestrated?)

So, on the whole, it shows a huge lack of perspective if you believe that McCarthyism was somehow novel or unique in pushing the idea that people's careers, especially public careers, should suffer if they commit certain ideological transgressions. That has been a permanent feature of American society ever since the New Deal, and the only question was who would get to wield the ideological hegemony and determine these bounds of acceptability. Therefore, I don't think it's justified to define McCarthyism by this aspect, when in fact it merely meant acceptance of the already established rules of the game. Sure, you may want to condemn all sides from some idealistic perspective, but believing that McCarthyism was really exceptional in this regard is merely buying into the propaganda of the winning side.

With that in mind, I do think it's accurate to see the struggle of elected politicians against the permanent bureaucracy (and its close allies in the media, academia, etc.), and the defeat of the former that firmly confirmed the dominance of the latter, as the central and most important element of the whole McCarthyist phenomenon.