The handling of this incident made me very angry, principally because it's so hard to get MIT students to seek mental health counseling because they are very fearful of retaliation for doing so. The misuse of the mental health survey totally validated their concerns and severely damaged the fragile trust that various orgs student health orgs unaffiliated with this incident at MIT had worked hard to build with students.
Also, this article does a poor job of explaining the recent history leading up to the closing of Senior House, which better explains why the closing of the house was viewed as a total attack on alternative culture. MIT didn't just close senior house, they also knocked down Bexley, another alternative dorm, a few years earlier under somewhat dubious circumstances (suddenly refusing to repair the dorm post flooding iirc?) without proper student input, and I believe there was controversy about a third alternative dorm as well. The students' interpretation of this was that the MIT administration was fundamentally targeting alternative culture and were not negotiating in good faith during any of these closures.
In essence, if you use an institutional email account (or keep personal data on Athena or otherwise) you can presume administration will read it without permission. If you get into conflict with the Institute, personal emails can come up and be used against you.
MIT has a lot of good people, but "unaffiliated" is a difficult word to use here. The problems come from the very top of the administration. Just because a particular mental health organization is good and built up trust doesn't mean they have the power to not get overruled by the Central Administration later. Until and unless the Institute institutes some real checks and balances, students absolutely should go outside for mental health.
For example, I was at one point affiliated with an org that was dealing with sensitive student medical data and we had enough political power due to who we were affiliated with such that I don't think anyone could have tried to force us to disclose data.
The Institute owns the computers your data lives on. The Institute owns and has keys to the rooms where those servers live. The Institute believes it owns the data too.
What force do you think is needed?
Power at that level is rarely exerted at levels visible to a student or employee -- but it happens. I can't comment on your medical data, but most places, there are discreet channels for what the Institute considered to be more serious issues.