This is perceptive. As a society we must tolerate a diversity of opinions. Everything must be open to question and debate. But after questioning and debate, there must be a final disposition that lets us move on to other challenges. How we reached that disposition should be so clear that it invites renewed debate only in circumstances where new insights have been made.
I feel like we already use this pattern in a variety of settings. The legal system comes to mind, where we build this collective body of decisions that either prove useful and are built on, or modified and removed if not. But there is not a sense of anything being "inappropriate" to question. The very core of the legal system is challenged on a regular basis and we don't feel the need to censor those who challenge it. We have a general level of confidence that the system has checks and balances that let justice prevail.
Two observations. One is that this reminds me of eventually consistent systems. The law lags slightly behind reality but we know it catches up eventually. Reality is always changing and so we don't expect the law to always be up to the minute perfect. Perhaps we can embrace this notion of imperfection as a reason to keep discourse constantly open.
Second is that the law is effectively the source code for running society. It has procedures set up around it very similar to how we'd run a successful open source project. Integrators, reviewers, unit testers, engineers, project managers, pull requests …
Perhaps in the case of Yale and other institutions, what is needed is the same level of transparency we have in a well run source repo or legal system.
1) everything is written down somewhere, is properly attributed, and openly discussed.
2) systems are in place to propose changes, understand the impact of those changes, and integrate or reject those changes.
3) there is an understanding that this is an evolving system, it has a past, present, and a future.
4) history is recorded so that present and future discussions can be made with the appropriate context in place.
I feel like this is the solution for incorporating dissenting views, converging on the set of beliefs that identify the underlying priorities and preferences of the participants, and making it clear why certain things are the way they are.
It is entirely possible that institutions may converge around policies that are abhorrent to some, but being clear and transparent about that at least makes people know what they're getting in to. It's possible that a system like this at Yale would result in some students or faculty deciding that their views would not be welcome there, which is better than discovering that after the fact.