Come on... I think you are struggling to distinguish the two. Are you honestly of the belief that the wholesale incineration of tens and tens and tens of thousands of innocent men, women, and children -not to mention the abhorrent effects of the residual radiation after the fact- is somehow less heinous then the death of 2,000 suspected guerillas without due process?
I dont even think you can argue that with a straight face (one of the benefits of voicing an argument from behind a keyboard I suppose.)
Well, at the very least, the U.S's act was during an act of open war, it was an open act, and in its own way it wasn't much different from simply mass-bombing the city. Kind of like Dresden. And, well, I'm not about to condemn the use of bombers in wartime.
What Pinochet did, ignoring the numbers for a moment, what he did was turn against his own people by supporting death squads and underhandedly waging war, without checks or balances.
So the two acts are pretty different.