Unfortunately, democracies have their downsides. One of them is that "properly containing" things is extremely hard. Soviet spy network was vast and infiltrated all tiers of US society, and without instituting some extremely draconian policies, compared to which McCarthy would look like a hippie, I don't see how it would be possible to prevent it. Especially given a lot of top scientists were, unfortunately, if not communists themselves than quite friendly with communists and would probably refuse to cooperate with any draconian regime that would be capable of suppressing the communist networks.