As someone who's been in your son's shoes, I understand how he might feel awkward. I'd say it might be helpful to sit down with him and communicate how you're feeling... what you said in this post. Tell him the situation, and ask him how he would feel about you bringing your new wife. If he doesn't like it, or hems and haws about it, ask him what makes him uncomfortable. Listen to his concerns. At the end of the conversation, ask if there's a way that you could compromise, perhaps.
For example, maybe he feels weird about having pictures with you and her... in that case, maybe she could stand back when you go down to greet the graduates, and maintain her distance while the picture-taking and congratulating are going on, and then come forward when all that hullabaloo has ended. Not that she should be "standing in the shadows," but I think it's normal for a new step-parent to give you and your son a little space, while still supporting you as your companion.
That way, your son might feel more assured knowing that she's not going to jump into the pictures with you and him, or put him on the spot to acknowledge her as a new "mother"... which is probably the root of a lot of the pressure he's feeling (if he's anything like me, which I have no idea about).
All in all: talk to the boy!
