The best known example would be Hirohima/Nagasaki, and the moral justification for their atomic bombing is lacking
Perhaps. But at least in that case, the attacks were openly carried out by the military, with authorization from the President. The chain of command was followed. It wasn't a clandestine operation done by a secret organization answerable to no one. Unlike, of course, Section 31.
I'm sure the Federation has had times when it had to order Starfleet to carry out military missions that might be questionable. But in all of those cases, the chain of command was followed, there was debate on it, and there was oversight. I don't care if Section 31 even saved one life
- the mere fact that they don't answer to anyone, makes them automatically worthless and extremely dangerous.