Unfortunately for the student, he has not cloaked himself in any of the protective layers that allow offensive behavior to be "protected" speech. If he threw a Koran into a toilet onstage in the middle of a stand-up comedy routine, the cops would have no case. In fact, if he could argue that his action was in any way an artistic expression, he would be in the clear.

I'm not sure it's a double-standard, so much as a legal peculiarity. To take a less politically charged example, if I offer a nice lady $100 to have sex with me, I'm guilty of soliciting, and can be charged. If I ask a nice lady $100 to have sex with me in front of a camera, or on a stage, or while posing for a painting, I am protected by various legal precedents relating to freedom of speech and expression.

Likewise, if the guy who did "Piss Christ" had simply dunked a plastic crucifix in a toilet, he could be charged with criminal mischief and what have you. But instead he displayed a photo of his offensive act at an art show. His funding can be yanked, and he can be shunned by people of good taste, but he cannot be convicted of a crime.