They're not talking about "free expression" in the generic sense. They're specifically talking about Yale's Freedom of Expression Policy [1]. Comparing this to Yelp doesn't make sense, because the Dean of Yelp never said, "I disagree that Yale violated its policies on free expression in this situation." The policy in question specifically states that Yale values "the need to be able to 'think the unthinkable, discuss the unmentionable, and challenge the unchallengeable.'" and acknowledges that "such freedom may sometimes make life uncomfortable in a small society such as a college. But it also asserts that 'because no other institution combines the discovery and dissemination of basic knowledge with teaching, few need assign such high priority to it.'"

I don't really have a bone in this fight, so to speak, but I do find it interesting that the Dean of Yale has such a problem with the way their students are using their data to express an idea, when their very own Freedom of Expression Policy says:

Yale's commitment to freedom of expression means that when you agree to matriculate, you join a community where "the provocative, the disturbing, and the unorthodox" must be tolerated. When you encounter people who think differently than you do, you will be expected to honor their free expression, even when what they have to say seems wrong or offensive to you.

Although, if we're being pedantic, their policy technically states that they expect their students and graduates to honor others' free expression, not that they agree to honor their students' free expression.

[1] http://yalecollege.yale.edu/content/freedom-expression