> This is an unfortunate outcome, since Yale’s copyright assertion muddles the argument that Yale’s actions violate Peter and Harry’s freedom of speech.
No it doesn't. Whatever Yale's responsibilities in the freedom-of-speech realm may be, they are entirely ethical in nature, as freedom of speech in the legal sense refers only to what governments may not suppress. Holding the copyright to something does not in any way affect ones responsibility to behave ethically.
> If Yale grants students access to data, the university does not have the right to specify exactly how students must view the data.
Under U.S. law they may very well have the right; I wouldn't know. What you may have demonstrated is that they do not have the ability.
May I suggest that you do not couch your arguments in terms of fallacious claims about freedom of speech. Rather, talk about academic freedom, a principle -- though not a legal one -- that Yale ostensibly seeks to uphold.