The relevant question isn't whether, under the 1st Amendment, the student paper had a right to publish the editorial and the kid had a right to think those thoughts. It did, he did. The relevant question is whether the same student paper would publish an editorial arguing that high school girls who aren't virgins should be put to death because THE BIBLE! Or if the same student paper would publish an editorial arguing that infidels should be put to death because THE KORAN! I'm guessing the answer to both those questions is "no."
Why is there an exception for homicidal, sacred-text-justified hatred when gays and lesbians are the target?