The incidents I know about haven't been publicly exposed. If I spoke about them in specifics, the Institute would retaliate. One I can bring up -- since I don't think it exposes me -- is email.
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.