Note- continental European academia has different intellectual traditions and specific contexts, so will be kept out of the discussion.

Assuming the OP is giving an accurate picture of the poly sci prof's position the characterization that Marxism was "rampant" in the Anglo-American academy is both inaccurate and a gross oversimplification of the actual Marxism that was present inside the ivory tower.

Firstly, there is an enormous problem of periodization of the 1950s-1980s because between the 1950s and mid-1960s, the climate of universities was incredibly hostile both to Marxism and the Soviet Union. In the US, the climate of McCarthyism led to both loyalty oaths and the purging of faculty with perceived pro-Soviet biases. Furthermore, there was significant pressure from within the university faculty themselves to conform to the American side of the Cold War. For example, Armin Rappaport's appointment to Berkeley was held up because the chair of the department was concerned that he might "have some of the ultra left wing tendencies so common to the New York Jewish intelligentsia," and would only countenance accepting Rappaport into the faculty after he had given his word that he was not an opponent of American foreign policy. Nor was the administration of universities open to Marxist perspectives in this period. When in 1964, Berkley's history department unanimously invited the CPUSA member and academic Herbert Aptheker to address a graduate colloquium the administration denied funding for his appearance and refused him to speak on campus, forcing the history department to have him speak off campus with funds out of pocket.

It is not a coincidence that this early period of the Cold War saw the formation of some of the most virulently anti-communist interpretations of Soviet history and society. Not only did Hannah Arendt's notions of totalitarianism (i.e. that Communism and Fascism were largely indistinguishable tyrannies) find wide spread currency within the academy but so to did other anti-Soviet paradigms find fertile soil. Richard Pipes's 1954 book The Formation of the Soviet Union: Communism and Nationalism argued that the Soviet Union was a stalking horse for Great Russian hegemony and that instead of liberating the various nationalities, the Soviet state acted as a "prison of the peoples" for non-Russians. This interpretation, which dovetailed with ideas that the USSR was as expansionist and exclusionary as its tsarist predecessor, gained a lot of traction in academia and was one of the dominant interpretations in the west on the Soviet nationalities problem almost through the end of the Cold War. Nor was such anti-communism the sole preserve of the right. Left-leaning faculty could hew to the Cold War liberalism as exemplified by Arthur Schlessinger, jr. Cold War liberalism did not take a knee-jerk hostility to communism, but did champion initiatives to ensure that the Third World would remain favorable to free market capitalism. Overall, there was a consensus inside the academy in this period, with the exception of a few outliers, that containment of the USSR was necessary and that the Cold War was a zero-sum game; the Soviets' loss meant America's gain and vice-versa.

Marxist-influenced thought did not make much of a comeback in the academy until the advent of the New Left in the late 1960s, but it was often a form of Marxism that was not immediately recognizable compared to its forebears of the interwar period. In the field of history, some of the pioneering work done in the UK by the Communist Party Historians Group who pioneered an examination of history "from below' in the 1950s. The New Left could be myopic about the USSR's development and tended to take a pro-Soviet line in the Cold War. The Polish emigre Leszek Kolakowski famously engaged in a dialogue with E. P. Thompson where he perceptively argued that the New Left presented. "whatever bad happens within the "capitalist system" is by definition the product of capitalism; whatever bad happens in "the socialist system" is by the same definition the product of the same capitalism." Despite these tendencies to explain away the faults of the Soviets as highlighted by Kolakowski, the Soviet Union clearly lacked the allure that it had enjoyed in the interwar period as a mythical worker's paradise.

The part of the Communist world that did enchant the New Left was that of East Asia and the various revolutionaries in the Third World. This spilled over into scholarship in the 1970s in the aftermath of the Vietnam War where both China and North Korea seemed to offer a proper developmental model for the rest of the Third World that would be an alternative both to Western free market capitalism and an seemingly ossified Soviet Union. Theda Skocpol's monumental States and Social Revolutions which examined the French, Russian, and Chinese Revolutions took the Maoist line of "walking on two legs,” at face value, and argued that the PRC had achieved a balanced development of both the countryside and the urban areas with a strong emphasis upon responsible leadership at local levels, emphasis upon medium and light industry, and novel techniques to prevent urban over-crowding by taking measures to send educated urban-dwellers in the 1960s into the countryside. Somewhat more embarrassingly, some in the New Left championed the DPRK's Juche movement as a way to fuse nationalism with socialist development and treated the emerging cult of personality around Kim il-Sung as an aberration caused by the Korean War and tensions with the ROK. While there certainly was some cause for these rosy assessments, the economic growth of the DPRK was rather strong in this period and Park Chung-hee's authoritarian government had entered into a pretty nasty period of domestic repression in the 1970s, this rather blinkered view of the East Asian communist states had a marked tendency to ignore the repression and flaws of these polities. In the 1980s, R. J. R. Kirkby’s Urbanization in China: town and country in a developing economy repudiated his earlier work that suggested, like Skocpol, that China had a balanced economy and contended that “our own Western susceptibility to agrarian utopian and oriental fantasy” had produced a highly skewed view of Chinese economic development during this decade. Even Eric Selbin, whose earlier work on the Maoist Yenan Way contended that Maoism had managed to shape the countryside into a potent anti-imperialist weapon, has cautiously backed away from his earlier enthusiasm for this process and called such sanguine sentiments a reflection of "a more hopeful epoch," of world history.

But not all the Marxist thought produced during the 1960s ended up in a Maoist cul-de-sac. in the field of history, scholars like David Blackbourn, Eric Foner, and Donald Worster produced incredibly valuable studies in the early 1980s that are still highly influential. The Marxist (or more accurately, Marxist-inspired) arguments they present are quite sophisticated and do not talk about crude stages or other dross that would characterize an ideologically-driven version of history.

As for the issue of minimizing the faults of the USSR, the most prominent group in the 1970s that argued for Soviet success in the 1970s was the so-called Team-B of various anti-Communist intellectuals and government officials. Lead by Pipes and other anti-communists, Team B contended that the Soviet planned economy was far more successful than the CIA's more realistic assessments on Soviet strategic capabilities. While Team-B did not deny the reality of Soviet repression, they argued that such political repression was irrelevant to Soviet strength and power projection. This alarmist view of Soviet power, which tended to take Soviet claims of growth and face value and even exaggerate them, created a de facto erasure of Soviet repression by assuming that the average Soviet citizen had been cowed by terror and the state to obey. The reality of the USSR was quite different and Team B helped to blind many public intellectuals to the growing apathy and dysfunction of the Soviet system. Unlike the New Left or other left-wing intellectuals in the academy, these neo-conservatives had far greater access to political power, especially with the election of Ronald Reagan.

Are you in the United States? If so, your professor's statement seems a little odd, given that several hundred professors between 1948 and 1954 were fired, or had their academic careers derailed, either because of their affiliations with the Communist party or because they failed to cooperate with the House Un-American Activities Committee.

In 1948, the University of Washington launched proceedings against six professors suspected of communist affiliations, leading to the dismissal of three of them in 1949. The same year, the Board of Regents of the University of California imposed a requirement that all University employees sign an oath affirming loyalty to the state constitution, and also a denial of membership or belief in organizations advocating overthrow of the United States government - which included communists of various stripes. Several UC employees were fired because their unwillingness to take the oath, and others had difficulty advancing in their careers. Other states, like New York, followed suit in various ways.

Aside from the damage done to careers, some have argued that McCarthyism fostered an intellectual chill in academic circles that made researchers less likely to pursue controversial topics or adopt perspectives that might taint them as reds.

Certainly, this chill had dissipated by the 1960s with the rise of the New Left - spearheaded by academics who were often decidedly socialist/Marxist in their orientation - but I think it's very misleading to hold that Marxism was in the mainstream of academic thinking in the 1950s.

For more on McCarthyism in academia, see the work of Ellen Schrecker: http://www.lib.berkeley.edu/uchistory/archives_exhibits/loyaltyoath/symposium/schrecker.html