Protests don’t really work if they’re not disruptive.
At the same time, any legitimate authority has a vested interest in minimizing disruption.
It's one of those things where I think neither side is inherently in the wrong, at least insofar as the question of "Protest vs. Disruption" is concerned. One must protest for what one believes is right, even if that protest must be disruptive to achieve its goals, and one must be prepared for a response from the authorities if that protest is sufficiently disruptive. You have to break rules, and you have to accept that the authorities are not necessarily wrong in trying to enforce the rules.
Short of saying "Only people I like are allowed to protest" or "Republicans can shut down the interstate highway indefinitely because they hate gay marriage", neither of which are particularly appealing, I don't really think that there's another option.
That this is all done by universities in the defense of a genocidal apartheid state, though? Not very morally ambiguous. This isn't a minor policy disagreement, or even a major one. This is support of corruption in US politics, the blatant sabotage of US interests abroad, and apartheid and genocide in Israel. Fuck these places trying to run interference for Israel.
The dynamic still holds as valid. It's just that the universities are shitty fucking authorities for taking the side that many of them have.