There's a couple of different questions here. One is "Should students be punished for protesting.' The other is, "should schools be punished for students' protesting." My answer is no ... they should not be punished for meeting up, carrying signs, singing songs. But that isn't civil disobedience, it's peacefully expressing their opposition to a war, or anything else they feel strongly about.
When you introduce the concept of civil disobedience, sometimes getting arrested is the *whole point*. No - getting *photographed* being arrested is the whole point. Cops bodily carrying away "innocent" cross-legged protesters" is the image you want to promote. Rosa Parks planned to get arrested and was selected for the role partly for her clear head.
But if your civil disobedience includes, for example, blocking traffic in a way that impedes emergency vehicles, and there is a law or policy against that, the individual in the road should be asked to move. Calmly, preferably by someone trained in negotiations. If someone who appears to be a leader says, "We'll leave if the dean comes and talks to us," try to get the dean to talk to them. If people stay in the roadway, begin making arrests. They may decide they've won at that point. Don't lose your temper, even if rocks start flying from all around. Announce,
"if violence persists we will use teargas to clear the area." Oops, here comes another rock. OK, here's the teargas. Let the arrests begin, because all of them have been told to disperse due to public safety concerns.
What I've never understood - I will look for myself, but if you have anything, great - is exactly what is being said and done at these protest. All the time I was hearing about anti-Semitism I wondered how many Muslim students were dealing with Islamaphobia. "Ceasefire now," "I stand with the Palestinian people," "Let my people go," even "Stop the genocide" are fine with me. Not fine: death threats, obviously. I personally do not equate anti-Zionism with antisemitic, but it's very easy to cross the line between the two sentiments.
If hate speech against Israel/Jews/Zionism is not tolerated, neither should hate speech against Palestinians, Arabs or Muslims. I've seen plenty of people saying Islam should be eradicated and Israel should "finish the job" by letting Gaza starve. I would imagine the Constitution would protect most of these phrases, but if there are university rules against such speech, schools should enforce them evenly. And inciting violence may be a crime despite 1A protections. I find it hard to believe that Muslims haven't also experienced a ****storm of hate but I haven't really researched it.
BTW if anyone says "they elected Hamas" - I have calculations somewhere indicating that only 6 percent of Israelis now living ever voted for Hamas. Can't find them at the moment.