As for 2: https://en.wikipedia.org/wiki/Battle_of_Athens_(1946)
As for 3, no one is suggesting it become a routine method. Heck, the early 20th Century Imperial Japanese political culture of assassination and what it led to is a stark object lesson (particularly stark as I finish reading this right now: http://www.amazon.com/Hell-Pay-Operation-Downfall-1945-1947/...)
As for 4, your history lessons must have skipped this event: https://en.wikipedia.org/wiki/American_Revolutionary_War
Overall, it's rather interesting you can't conceive of the deterrent effects of a well armed populace. Surely our 21st Century experiences in the sandbox suggest something....
It had many interesting revelations, including the single thing which had a higher priority than the Manhattan Project: the building of a super-Mullberry for Operation Coronet, the invasion of the Kanto Plain on main island of Honshu, where Tokyo and much else was located.
And if you study the endgame on the Japanese side, it's really not likely nukes in Tokyo harbor to scare the shit out of the population would have worked, for one thing, they had no say in the running of the country. There also wasn't generally clean separations between military installations and civilian areas, especially since Japan is so crowded.
No, one of the clear factors was their leadership realizing we'd advanced to the point where a single plane could destroy a city, instead of requiring near Maximum Efforts with hundreds of them.
And of course, the bottom line is that these bombings worked. All else is speculation.