I would say the debacle was worsened[1] due to poor communication on everyone's part, but the professor focused on a topic that was not the main complaint of the students (the prof was also officially hired in a prestigious mentorship position, with expectations to listen to comments about bullying/racism/sexism). Most people agreed with what he said about free speech, but the main complaints about consistent casual racism (comments only tangentially related to the stupid letter that started the discussion) were never responded to. A simple acknowledgement that "yes, I now see that you face casual racism on a daily basis here at Yale, so let's work together on educating people about this casual racism" would have probably defused the situation.

[1]: I mean, just see all the sibling comments that assume this whole thing was about some stupid letter about costumes, and everyone calling all the students childish and dismissing their legitimate concerns (not even trying to find out what these concerns were) because they have seen the reaction of a couple overly-emotional students on YouTube.