Agreed. Wear the uniform, if you like... with the cap and gown over it for the ceremony. If he doesn't want to do that, or if that is some sort of breach of Marine dress etiquette, then he can sit out, like he did.
I'm sure he's a great kid, but graduation is not the place to dress in what you want.
When I graduated college, there were dress blues, dress whites, and army blues. Of course, we all wore uniforms.....