Again, we're talking about students on school property. There are a LOT of things that even I, as an adult, cannot do on school property. These same principles carry over to any kind of school sponsored public event.
The thing of it is, is that the school has to worry about frivolous lawsuits. Most schools don't have the money to fight lawsuits so they take certain precautions to make sure that it doesn't happen, and the Supreme Court tends to think that it is okay. If the students are allowed to hold private prayer group during school hours on school grounds, then the school IS trying to honor their right to practice their religions, and it is not unreasonable for the school to expect their students to follow the rules and submit speeches and things to them in the appropriate way.
Another point you made earlier about children having equal rights as adults is just not true. For instance, if my mother held me in her home against my will, that would be considered kidnapping because I am an adult. However, if I was 12 or even 17 years old, my mother most certainly COULD hold me in her home against my will. I would not have the same rights that I possess now as an adult. I know that's not relevant, but I was just using it as an example of how rights of kids and adults can differ greatly.