While the proposed punishment of the teen (including a felony charge that can result in 2-8 years in prison) is most certainly excessive, he was arrested not for the doll, but because of his behaviors as seen by a janitor and the security cameras outside the school whose footage was reviewed after the janitor reported what he saw.
The teen went in wearing a hoodie and latex gloves to conceal his identity, carrying a package under the hoodie. When he emerged from the school, the cameras saw that he didn't have the package with him any more as he was leaving the area, which he did not at a leisurely stroll but in a hurry.
While the town is sufficiently "small change" enough that the notion of a terrorist attack there is dubious at best (and that's being generous), outside of those living nearby how many people had heard of Columbine, CO before those two f-wits went on their rampage? Remember that part of their plan originally included detonating multiple pipebombs in the school.
As I said, though, the charges are certainly excessive, but without reading the law under which he's charged I suspect that sloppy, overly broad law writing was involved, along with school administrators being idiots by applying the law in a way it wasn't intended by the legislature, and unknowingly invoking the Law of Unintended Consequences.