I think you have brought up a very tricky thing to navigate. Definitely, students should be allowed to protest and have the right to free speech, but this. I believe, would only work if we consider universities to be politically neutral institutions. Ideally, universities should, as you have said, be safe places where one cane express their opinions and hold onto their beliefs without harrassment and coersion from external and internal factors. However, many universities have highly problematic origins, things that have been brushed under the rug rather than being aptly dealt with. In addition to this, donors and major financial contributors for many universities all over the world have very morally grey foundings and rises to fame (for example the Rockerfellers and other old money families like the Carnegie's). These donors then have a lot of say over the proceedings of universities, and many are then included in their board of trustees. I think that along with the problems you have highlighted, this becomes another very important problem in allowing for freedom of speech.
I've also explored how problematic money and philanthropy in education can be in my blogpost here, I'd love to hear your thoughts!