Freedom for scientists in the Stalin period depended heavily on their field. The Soviet academy was highly politicized under Stalin, along complex ideological lines. If your work subjected you to possible political attack, by philosophers or other scientists, then you would have to be very careful.

There were many lines of attack leveled at scientists' work. A way to think about this period is less that Stalin was himself being heavy-handed about scientific content (though in a few fields he could be), but more that the Stalin period created great incentives for denouncing others and great fears of being denounced. You can think of denouncement as sort of a political currency, a form of free-circulating power. You could attack other disciplines, other rivals, other theories, or you could be attacked. It is less about "government officials" stepping in where they were unasked for, and more about other academics leveraging state power in various ways.

So the action of scientists was often to preemptively try and insulate their scientific content from attack. An example from physics: General Relativity came under the attack of philosophers as being bourgeois and idealist, connected in some vague way to concepts of moral relativity. Soviet Marxism has no real taste for that sort of thing (it believes in a world of absolute material truths that can be revealed from the study of history and economics). Several defenses of General Relativity were made by physicists in the Soviet regime. One not very effective one by Boris Hessen was to argue that scientific truth could be independent of context (illustrated by showing the deeply classist nature of Newton's work, which nobody doubted the truth of). A more effective defense was made by Vladimir Fok, who argued that General Relativity was merely a theory of gravity, and essentially removed all philosophical connections it might have, arguing they were just imposed by imaginative minds.

Biologists infamously had the worst time under Stalin and were a sort of warning beacon to other Soviet scientists. Genetics was co-opted by Trofim Lysenko, a charismatic agronomist who argued against Mendelism on (shaky) theoretical lines, but whose thrust of argument came from the fact that the academic study of Mendelism did not produce the kinds of quick results in agricultural production that the Soviet economy required. Lysenko promised those gains and the Soviet-state press ended up claiming he gave them. Stalin had some personal interest in Lysenko's arguments, and Lysenko's denunciations of Soviet Mendelians as "fly-lovers and people-haters" were well-tailored to the times, but scholars also generally emphasize that the triumph of Lysenkoism was inextricably related to the Soviet Union's collectivized agriculture policies, and they essentially chose Lysenko to be a "scientific hero" in the face of disaster. Anyone who continued to advocate Mendelism during the Lysenko period could face harsh consequences, including being sent into the Gulag. The case of Nikolai Vavilov, an eminent Soviet biologist who perished under Lysenkoism, is instructive.

OK, but what if you're not in one of those sorts of controversial fields, what then? Soviet scientists in many other fields — e.g. chemistry — took proactive measures to make sure their fields weren't going to end up getting overly politicized. They saw Lysenkoism and shivered. How to avoid something like that? Focus on the practical: make sure that the field is 100% focused on practical, state-centered, people-centered problems, and avoid all "pointless" theory. Such was the way towards safety, making your field look completely aligned with the state-sanctioned philosophy of dialectical materialism, which essentially says that the aim of science is to serve the material needs of the state, not to come up with anything too deep that might call the official philosophy of the state into question.

If a scientist did that, they could find themselves in very good conditions for science. Soviet resources for science and technology could be lavish — it was core to the early Soviet idea of what it meant to be Soviet, to be scientific and technical. (Lenin famously proclaimed that Communism was "Soviet power plus the electrification of the whole country," and there were numerous posters fetishizing things like dynamos, tractors, hydroelectric dams.) If you could hook yourself into that system, and produce useful things, then recognition, perks (a nice dacha, for example), and healthy respect were available. But it did require making sure you never were made to look like you were wasting anyone's time or resources, or were in any way disloyal to the Soviet state and program.

And if the work one was doing was truly of high priority to the Soviet state — such as that of the nuclear physicists after 1945 — then the perks could be very good indeed. However even these people were pretty "tame" during the Stalin period. Under later administrations they spoke up a bit more, as things loosened up.

As for exchanging ideas: Soviet scientists did publish in Western (non-Soviet) journals, and they did receive journals from abroad. International conferences during the Stalin years were tricky; there were some, but the Soviets were always worried about defection and so there were always several NKVD/KGB sorts of types sent along as "minders," and families were generally kept at home. Soviet scientists sent to conferences abroad were of intense interest to Western scientists, and their governments, and attempts were always made to have confidential conversations out of the earshot of the "minders," with a goal to learning about conditions back in the USSR.

For more reading, Loren Graham's Science in Russia and the Soviet Union: A Short History is a great introduction and covers a lot of this ground (e.g., there are chapters on Fok and General Relativity, and there is a chapter on Lysenkoism, and one on dialectical materialism). The classic study on the workings of power in the context of denunciation is David Joravsky's The Lysenko Affair.