Talking past each other, no doubt. There are a lot of separate but related issues at play here:
1) Whether the "clock" really looked like a bomb;
2) Whether the "clock" could be reasonably taken as a bomb by people who didn't know better;
3) Whether the kid knew or should have known it would be mistaken for a bomb;
4) Whether it had any other reason to be there;
5) Whether the school should punish kids for possessing things that look like weapons but turn out not to be;
6) Whether doing so is consistent with other zero-tolerance cases;
Any reasonable person's reaction to this news story would be like this:
1) Reading initial news articles that don't show a picture of the bomb: poor kid
2) Seeing the photo: that looks awfully like a bomb
"It's a pencil case" excuse is pretty weak. If he put the clock inside a bomb-shaped pencil case, would people still be defending this kid?
Probably the most successful trolling that I've ever seen - visit to the white house, props from some of the wealthiest men in the world, donations - this kid is amazing.