You are exactly right. It does not justify violence. However, where are you going to draw the line on what's 'ill' treatment? If I looked crossed eyed at a gay student, would I be allowed to graduate, without passing a tolerance test? Would I be expelled if I said, "I think homosexuality is wrong."? People DO have a right to be safe, and those rights & laws are already on the books. If I beat up someone because they are gay, I'm wrong. Actually if I beat up anyone, I'm wrong.
If you tell me I can't say "I don't like them" you are wrong. I have a constitutional right to say it. That's what you want done isn't it? You don't want children and their parents to be able to say something or believe something.