I tend to be of the opinion that public schools shouldn't censor students without good reason. In private schools, anything goes pretty much.
But I'd call this a good reason, and a case of dress codes working well.
Those t-shirts, while falling under freedom of speech, don't even seem related to religious expression to me. It's not like bashing Islam, let alone openly, is a major tenet of the Christian faith and something that all Christians must observe. If you're going to flaunt your prejudices, don't use religion as a cop-out.