Schools can already have their newspapers edited by the principal, so I don't see why people are screaming now.
Free speech was never absolute in primary and secondary schools, so it should come as no surprise when this ban occurs. This is not a permanent ban anyway, it's most likely temporary until the tension lays over. This is a school first, a place of learning, where you learn about math, science, english, etc. The display of any flags at this moment isn't to show patriotism or to show solidarity, it's the equivalent of sticking your tongue out at others.
Schools will ban something when it is apparent that you're wasting too much time trying to enforce a rule. They don't allow chewing gum, no one says anything, you can't wear a hat, no one says anything, no they ban the flags temporarily, and there is an uproar? When you're having groups of students fighting over somehting as small as a flag, remove the flags and get them back to learning.
I think complaining about the ban is useless because you're forgetting the purpose of school in the first place. If the students all feel this is so wrong, they should collectively stage a walkout. That won't happen because we know the flag display was about raising tension, something you don't have the right to do.