Thinking from a moral prespective, the guy in the article would not have a good reason to to this. But let's consider the circumstances:
Graduation is a school function, and is sometimes mandatory. Even if it isn't, Graduation is an important ceremony in a kid's life. Missing it would definately be a blow to their morale in the future. So he either attends and has to pray to a god he doesn't believe in, or miss a once-in-a-lifetime ceremony.
Now, from a legal standpoint, this kid is in the right. Seeing as it's against State law, the school is in the wrong, as are the people who are trying to get it put back into the ceremony. If I were that kid, I would've just sued, or contacted the State and the ACLU about the school breaking the law, and watched the punishment ensue. I would have prefered suing, though. More money that way.
Freedom of Religion is fine, but not when your idea of "freedom of religion", is freedom to force your religion upon other people, in an environment where, even if it wasn't forced, it would be against the United States Constitution anyway, as it results in a violation of the seperation of Church and State.