I preface it here by saying that this argument is not new. Whites argued during Jim Crow that integration would unfairly abridge their right to discriminate. Rights must be balanced based upon real-world outcomes. It really does violate a restauranteur's rights of freedom of association to say that he must serve all races. The supreme court decided that rights violations endured by african americans was greater than rights violations pushed upon racists. As was once written, the right to swing your arms in the street ends at another person's nose.
Forgive me for saying so, but it's quite obvious from your reasoning that you have never experienced the sort of discrimination that befalls minority groups.
There are people in the world who do not appreciate being told that anti-semitism is wrong and there are people in the world who do not appreciate being the only Jew in their school and hearing every day about how they are going to hell and about how the holocaust was just fine and dandy.
There are people who don't appreciate being told that homophobia is wrong and there are people who don't appreciate being utterly isolated and enduring daily threats of physical violence, general social ostracism and ongoing sexual harassment.
Conflicts between minority groups and majority groups are not meetings of equals. Discrimination implies power inequality. Children exhibiting racism are hurting the object of their ire in a way in which racists would not be hurt by having their beliefs altered.
You may think it possible for somebody to believe that an individual is sick and disordered and going to hell and destroying society and to still treat their object of contempt with respect, however, I find this to be very unlikely even with sophisticated adults. Certainly not with kids.
It may violate some sort of dubious rights to force people to confront their prejudices and help them overcome them, but it very definitely violates the rights of minority groups to force them to "tolerate" harassment. You say forcing tolerance of difference is bad, but this explicitly allows tolerance of racism. In the first case, you are forcing an oppressor to tolerate a group they see as beneath them and which, likely, they have some social power over. In the second case, you are forcing a victim to tolerate abuse.
A classroom discussion wherein one student who is in a privileged position says something negative (perhaps hypothetical or theoretical) about a minority group, is directly harmful to the members of the minority group. Hypothetically, you think all gays are objectively disordered. Joe in the corner is gay. Joe just heard somebody in class say that HE (Joe) is objectively disordered and the teacher said nothing to counter it. Joe takes this personally and the teacher implicitly endorses this judgement.
What about freedom of speech? Well, freedom of speech does not include sexual harassment. Freedom of speech does not include bullying or teasing. Freedom of speech should not include making disparaging remarks that apply to other members of the community based on immutable characteristics without those remarks being challenged. Challenging the remarks is challenging the belief that spawned them.
You argue for some sort of freedom of thought. What is thought without speech? You can think that gays are evil and disgusting, but you can never let anyone know what you think? Is your right to hate gay people greater than the right of gay people to be able to go to school? Since gay people are targets of discrimination, to say that those rights are equal is to say that gay people do not have rights.
To say that whites have the right to be racist is to say that blacks should not be able to frequent all businesses and apply for all jobs and got to all schools. Speech is a form of action. If I put up a sign in a restaurant which says "whites only" I have taken a definite action through my words.
You got over your queerphobia because your friend came out. In cases where homophobia is unchallenged and allowed to continue unchecked, it is much more difficult for gay people to come out. If some social changes (whether in general society or by a conscious decision by your school to fight homophobia) had not occurred, Nyssa might have stayed in the closet, or, like ONE THIRD of gay kids in 80's she might have tried to killed herself.
I was the first out person in the history of my catholic highschool. Teachers did not challenge homophobic statements made by students because of some sort of "morality" issue. I got beat on in gym class. I got sexually harassed continually in some of my other classes. I took is very personally when people said "[all] gay people are (sick|wrong|perverts|child molesters|...)." This is not hypothetical. This is a deeply hostile classroom environment which makes it very difficult to learn, which lead me to contemplate suicide, which lead at least one of my friends to attempt suicide.
Letting individuals grow in whatever direction they find satisfactory may or may not be a noble goal (I'm not sure that it is. There are cultural memes like "reason" that should be propagated), but we live in the real world and need to think about how these ideals would be realized in the ugly, dirty worlds of high school and junior high.
One third of gay teens in the 80's attempted suicide. Some lower number were successful. A very high percentage contemplated it.