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.
I think if you look at the type of continental movement that was made by the marxist guerillas during the late 60s and 1970s, which was made with outside support and funding btw, you would be remiss not to conclude that there was an "open war" going on. So again, I think you are making a distinguishment without a difference.
Second of all, you wont condemn bombers -which until precision guided munitions have generally been indiscriminate purveyors of death and destruction- but you voice outrage at ambigously defined "death squads" and "underhanded" warfare. Again, a distinguishment without a difference.
Lastly, you are so quick to "ignore the numbers," WHY? You claim the acts were pretty different, but you only view them that way because you dont want to condemn arial bombers and you do want criticize Pinochet. The bottom line remains that we killed 100,000+ innocents -an act which your ok with because you consider the context- and he executed 2,000 without due process of law to win against an insurgency that would have installed a communist regime.
Why dont you afford him and his actions the same historical context and consideration in making a judgment?