If the gun were unloaded & encased, he couldn't be charged with the GFSZ "violation", nor with improper transport (assuming he came to school in a car or bus). Could explain why they didn't throw those at him. [See 948.605 (2)b3(a) for the unloaded & encased GFSZ exception.]
And if it was encased & they do keep the CCW charge, maybe this will finally be the test case to delineate (sp?) between concealed & encased. (Which is one reason the DA didn't charge me with CCW. He didn't want it to be a test case.)
He could, however, be charged with 948.60 - "posession of a dangerous weapon by a person under 18" (a misdemeanor).
I don't think the DC charge should be on him (all he did was show another kid some ammo; there's no report that he displayed the gun nor threatened anyone), nor do I think that he needed to be held in jail for a couple of non-violent misdemeanors.
Although if that were me, I think maybe a couple nights for my parents to cool down before I went home with them would be a Very Good Idea, & I'd still expect to be eating standing up for a day or so. (That being said, I regularly carried & used a pocketknife at school, in full view of teachers, and nobody ever said boo. These days even that is enough for police involvement & a suspension.)
His parents are probably also considering the benefits of a gun safe, and making sure the kid doesn't know the combo or where the key is until he's had some training & shown better judgment.