Nordhaus's position to me seems to be stronger than you make it out to be. Here's the thing: even in the Soviet repression some academics risked their lives to speak out. You'd expect at least that much speaking out then among academics in the relevant fields when all they have to risk is their academic careers. Yet, in the relevant disciplines, one doesn't see much of any at all.

The trouble is, the situation is fundamentally different here. If there existed some sort of crude open attempt to dictate official dogma, as in the Soviet Union, I have no doubt that a small but still non-zero minority would speak out against it, no matter what the consequences. However, in the modern academic system, there is no such thing -- rather, there is a complex system of subtle but strong perverse incentives that lead to systematic biases and a gradual drift of the academic mainstream away from reality. (Of course, the magnitude of these problems varies greatly across different fields.)

In this situation, a contrarian is faced with a situation where making fundamental criticism of the state of the field won't invite any open persecution and accusation of heresy, but it will lead to professional marginalization and ruined career prospects without making any useful impact at all. After all, is there a more surefire way to get derided as a crackpot than to claim that accredited experts are failing to appreciate your insight? (Of course, in a field where the mainstream is correct, like in most of the hard sciences, this is a perfectly good heuristic.) So the choice isn't between conformity and heroic defiance, but between conformity -- best achieved by internalizing the mainstream biases -- and becoming a marginalized crackpot who invites only ridicule by anyone of any consequence.

Now, all this may sound like theorizing without evidence. However, in practice we do see whole academic fields where even a basic rational scrutiny of the academic mainstream shows that it's seriously divorced from reality -- and yet, we see no academic insiders screaming this awful truth from the rooftops. The occasional contrarians who mount fundamental criticism do this with a tacit understanding that they've destroyed their career prospects in the academia and closely connected institutions, and they are safely ignored or laughed off as crackpots by the mainstream. (To give a concrete example, large parts of economics clearly fit this description.)

Similarly, if repression of some form were serious, one would expect that the tenure system would cause more people to be free to speak out and one would expect a lot more vocal expressions of dissent from tenured professors than non-tenured faculty, but there doesn't seem to be such a pattern.

This is true only under the assumption that the tenure process doesn't screen thoroughly for people who have internalized all the mainstream biases deeply and honestly.

Mind you, this isn't as outrageous as it may sound. Consider for example a physics department that grants tenure to someone who is in fact a secret (say) relativity crackpot, and who then proceeds to peddle his nonsense with an inalienable academic title and departmental affiliation. This would be an absolute disaster, so physics departments can be expected to weed out prospective tenure candidates ruthlessly if they show any inclination for believing crackpot ideas, and you can't blame them for it.

Now, consider the same problem in a field where the mainstream is heavily biased. A department in this field is faced with the same problem, except that now the dangerous "crackpot" ideas may in fact be closer to reality than the mainstream. However, there is no independent outside authority that could ever confirm this: the biased mainstream consensus is, by definition, what all the credentialed high-status experts will say, and what the general public will use to decide who is an expert and who a crackpot. So a tenure candidate again gets weeded out at the slightest sign of ideas outside the mainstream bounds, except that now these bounds are seriously remote from reality.

Of course, it's always possible in principle that a contrarian might completely hide his views until he gets tenure, but such a grand feat of duplicity would be far beyond ordinary human powers. (Note that the bias of the mainstream experts doesn't at all mean that they are stupid!) It's also possible that a tenured exponent of the orthodoxy might change his mind under the weight of evidence, but people will very rarely accept a truth that places their life's work and accomplishments in a negative light. (Not to mention all the positive incentives, far beyond the guaranteed professorial title and job security, that tenured professors have for maintaining good standing with the mainstream.)