Students in the 60s waged sit-ins and were arrested. They knew that they would be because they were blocking the ability of campuses to function. Some of the demonstrations became violent, sometimes due to over zealous protesters and sometimes due to COINTEL infiltration.
But, even peaceful protesters can be arrested when they obstruct access to parts of a campus, or when they refuse to move after being told to because they lack a permit or administration consent.
Add to that threats and intimidation toward a specific group of students and there is another reason to tell protesters to disperse and arrest them if they refuse to.
Peaceful civil rights protesters for Black voting rights and integration faced much worse consequences than today's anti Israel protesters are facing. The civil rights protesters knew that they were breaking unjust laws, did it in ways that did not harm or threaten anyone (except for the egos of racists). They were not just arrested, but were beaten, hosed, had dogs turned on them, and fires set to buses while they were inside of them. Sometimes they were murdered.
A supposed right to obstruct campus functions, block access to parts of the campus, and intimidate select people is not guaranteed in the first amendment. Therefore, the arrests.