I wouldn't shoot him. Hear me out, though.
I'd get a bomb disposal team in to defuse and destroy the bomb, or his explosive charges, or whatever he's using to detonate it. Then, I'd torture him slowly, with a knife, over a very long period of time. I'd enjoy it, and he'd die eventually, so that way I get my revenge, plenty of fun out of it too, and the thousand people all live.
Failing that, I'd stil torture him to death slowly, but I'd make sure that the thousand people were all murderers and rapists and child abusers, so they deserve to die.