It makes no sense to blindly apply free speech principles based on majority/minority. By that logic we ought to amplify the voices of neo-nazis and other undesirables simply because they're a minority that would otherwise go unheard. To the contrary, I believe we're better off banishing them from the campus instead.
I completely disagree with your characterization of hate speech as speech that causes "subjective discomfort". Specific types of speech can do a lot of harm to e.g. individuals who suffer from mental illnesses or PTSD. So organizations have to choose. Either you ban the speech that will predictably harm individuals or minority groups, or you allow all speech (including hate speech) and the more vulnerable people will be forced to leave to protect their mental health. That's the reality of the situation. I don't think this is a difficult choice.
In practice free speech restrictions on college campuses don't restrict scientific work or scientific debate (in the broadest sense), so I don't think there is any cause for concern.
How about just blindly applying free speech principles? That's kind of how the "free" part of that is supposed to work.
There would be some hope of that if university students and admin had the slightest awareness of the 'Streisand effect.' They don't and they end up raising awareness of speakers and ideas they are scared of. It's comical. Free speech wins eventually, and that's net positive.
It's true that a lot of people are only hearing about this because of the protest, and that some of the public reaction is negative, but that doesn't necessarily mean that they would have been better served staying quiet.
Maybe hate groups are perfectly capable of getting the attention of their targets and supporters already, and getting the public's attention is the best way changing the status quo and reducing silent acceptance.
In reality, people protest because it works, even though they have to draw attention to the behavior they want to put an end to. The hope is to persuade the majority that they are righteous and the other side is in the wrong. That's how you get change. Sometimes the protesters mess up and end up looking bad. Then they lose credibility. That's OK, because then a different group of activists will stand up and continue pushing forward.
Safe spaces, micro-aggression theory, and other progressive concepts are quickly becoming mainstream, and they're definitely here to stay.
Until the next generation rebels against them. It's already happening.
The Streisand Effect relates to things someone doesn't want others to know about. If a protest isn't about supressing ideas or information then the Streisand Effect is not relevant.
What happened at this university is no different from a secretary deliberating forgetting to book a hotel room for the person they like least in the group. No different from the clerk at the DMV sending you to the back of the line because you made a paperwork mistake.
Where is the moral panic about this type of petty nonsense? Nowhere! Because we recognize it's petty nonsense, and not worthy of hand-wringing commentary or a national conversation. But when it comes to students and free speech and safe spaces every news channel and every major magazine is talking about it like it signifies the end of Freedom itself. It's totally absurd.
I think the difference is that petty nonsense on college campuses is publicized and quasi-institutional. If, somehow, a DMV employee was publicly and proudly making people they don't like go to the back of the line, and they had powerful people aligned with them, there would be some outrage.
While a few overzealous activists are not going to end Freedom itself, I (and apparently many others) still want to confront petty nonsense when it begins to institutionalize (by being supported by faculty/admin or influential media members).
What about a county clerk refusing to sign legal marriage certificates for gay couples?
Any serious talk about free speech should focus on the core issue: people in power abuse their power to punish the powerless when they express themselves in the wrong way. Students have practically no power or influence in society. So even if these "SJWs" are entirely unjustified in their actions the impact on society is utterly negligible. This is why the panicky reaction in the linked article about student activists repressing free speech is so comical. If anything, the student activists increase free speech by giving a platform to those people who would otherwise go unheard.