I do not live in the US and nor do I know much about the discussion surrounding this topic. At the start of your post, my first reaction was that what the Dean’s letter says makes a lot of sense. A lot of the ‘intolerance’ problems in the world today are probably because people having these problems grew up in ‘safe spaces’ and are just not geared accept other views.
But the remainder of your article demonstrate the point you are trying to make. And I agree. If we say that these ‘safe spaces’ are more like ‘moderated spaces’. I use reddit.com a lot. There are no safe spaces on reddit. And some of the best sub-reddits on reddit work well because they are moderated extensively. Rules for sub-reddits are defined — for instance, /r/nosleep says that everything that is said in the posts must be believed to be real, and therefore any comments questioning the authenticity are removed.
Schools, universities, and society in general should provide safe spaces — but more in the guise of clubs or moderated spaces (which I think is what you are talking about) — where rules are well-established and enforced. But it should be clear to everyone that it is only in these sandbox like environments where these rules apply and out in the real world, there are no safe spaces.