Except McCarthyism was an utter failure in terms of rooting out spies. We sure did so great, blacklisting a bunch of hollywood actors and narcing on our coworkers who just wanted a union. God forbid we have free speech and association right?

Meanwhile the actual Manhattan project was chock full of soviets.

McCarthyism is just what happens when you listen to paranoid demagogues. It was literally a culture war against liberals. Gee, sounds familiar.

Wasn't the blacklist unilaterally implemented by the heads of studios? It's not like Congress disallowed those people from working.

Manhattan Project was 1942 ~ 1946, while McCarthyism was 1947 ~ 1959.

Contributing to the rise of McCarthyism was: >a growing obsession with perceived dangers posed by internal subversion in general and Soviet and Communist Party espionage in particular, fueled by reports, some public and some held within the government, of Russian spy operations in North America, accompanied by a new Communist "hard" line that echoed general Cold War tensions;

So, correct: The Manhattan Project(full of academics, some(many?) of whom happened to be liberal) was as you put it "chock full of soviets" and the natural reaction to that realization was to clamp down on liberals.