The FBI knew all about Oppie's pre-war leftist sympathies and communist flirtations and they briefed Gen. Groves on it. But Groves knew that he needed Oppie to get the vital questions answered. Groves did not hesitate to come down hard on Oppie if he needed to yank some chains of some of the more "questionable" scientists.
The other thing to remember is that during the duration of WW II, we were the ostensible allies of the USSR. Thus, commie spying was viewed with less alarm than Nazi spying would have been (at least by the New Dealers who were running the war effort). The real reason Oppie's security clearance was revoked was because he didn't want to work on Teller's "Super", i.e., the H-bomb. He had outlived his usefullness.
I don't know how much of the communist infiltration of the Manhattan Project can be laid at Oppie's door. Anytime you get a lot of pampered, entitled academics together, you'll find a lot of leftist sympathies. The thought at the time was that we needed the bomb -- an we needed it yesterday. Other considerations were given less weight. Perhaps that was a mistake, but I relegate it to the "fog of war" symdrome, not conspiracy.
Normally I like your posts but you're way off the mark on this one. These guys figured out that a bomb could be made, got the government to fund the project, and did it. If they'd been chosen on the basis of their politics instead of their ability where would we be?
You also seriously misrepresent their politics. For the most part they figured the public - the world over - to be a bunch of boobs with very few worthwhile ideas about anything. They were very worried about putting an atomic weapon in such hands. Most of them were torn about the work they were doing but felt they had no choice - the genie was out of the bottle and our opponents might get the weapon before we did.