I try to see things from both sides, so this is what I think:
First, this child has every right to be called "Storm" if that is his legal name. However, this is probably the first of many "situations" if he doesn't make it his first name. What will he put on his resume? If it's Alexander Storm Longpolishlastname, that's what his interviewer and later bosses will likely want to call him. Many bosses would be okay with the change, but I could foresee more problems like this. If he is planning on being "Storm" forever, he should just change it. He has as much right to be "Storm" as he does "John" - just because it's not standard doesn't mean it's not a real name. If it were offensive, the government would not allow it to be a registered name.
Secondly, teachers have students try to pull a fast one. I am a teacher and I have students named Michael, Susan and Ashley who tell me they want to be called "Che", "Si si" and "Vita" and I say NO-- not in class. Now, if one of those names were their middle name and I had documentation, I'd have to go with it. If the teacher didn't have any documentation that stated "Storm" was his real middle name, he might have thought it was a joke, or that he'd lose credibility by going along with it.
I don't know the teacher's exact words, but it would have been best to ask him to talk to him on the side between classes and ask him to show id with his full name. Speaking professionally is a must for a teacher. I would also tell your son if he has any issues in the future to just smile, act polite and professional and offer to show identification if it is a problem. If after showing id, the teacher still has a problem, then it's a different situation and you might want to get involved.
Lastly, I think it is great to be involved in your kid's academic life. I don't think it's being a hovering parent at all to go to school over an issue. He's a freshman and at that age, I think it is still very important (maybe even more?) to go to parent teacher nights, check report cards, and stay involved.