I think that you should let him. Are there crossing guards at the lights?
If you let him walk, and he's a confident bike rider, then I think he'll be safe. Obviously you'll want to lay down the law about going straight to school and straight home and if he doesn't wear a helmet he loses biking rights for the rest of the year.
Honestly, I totally get the fear that a lot of moms have expressed, but I think that it's mostly unfounded - the vast majority of kidnappings are a friend or relative. There's millions of kids, and more than 99.9% of them don't get snatched on the way to school. We just hear about the ones that don't make it, of course. After all, do you think he's going to be ready to fend off an attacker at 10? 12? Realistically, he probably wouldn't be big enough to give someone a fight until he's 13 or 14 years old, and are you really going to walk him to school until then?
Anyway, that's just my 2 cents. If there are other cars and people around, let him go. Practice a few times before school starts with you. Good luck.