Let's see:
1. I wouldn't say that we 'bombed them out of existence'.
Perhaps not, but the cities to be bombed were chosen specifically because the geography of the area was such that the blast will be contained into the city, ensuring the highest possible number of casualties. That's just...cold blooded.
So, it can be said that the american planners did everything they could to 'bomb out of existence' the cities, by using an atom bomb.
Actually, I do not agree that their objective was to bomb either city out of existence.
Their objective was to make such a massive impression on the civilian population of Japan that they would turn against the Emperor, if necessary, in order to stop the war.
The Emperor of Japan - at least at that time, was regarded as a near-deity, and the population conditioned to regard his word a divinely inspired 'law'. Bombing things like military bases was to be expected, and could even be explained or hidden from the population, to a certain extent. And further, what would it accomplish? It was WAR. Soldiers die. 'Soldiers dying' was not something that would put terror into the hearts of the citizens of Japan to the degree required to turn them against a leader whom they regarded as divinely installed, and stage an uprising, if necessary, in order to force their own government to surrender.
2. There is some debate about whether the situation was 'desperate' or not. I think in the end it depends upon your definition of 'desperate'. It is true that the mainland of the US was not in eminent danger...and it is true that we were not in danger, at that point, of losing the war outright. However, a case can be made for 'desperate' in the sense that it was well known that Hirohito had no intention of giving up, and was ready to have Japan fight to the last man, if necessary. Winning the war, then, would have required an amphibious (ground) invasion of Japan - ships and planes alone were not going to do it. Since a ground invasion of Japan would have been an EXTREMELY bloody affair with massive casualties on both sides (some have argued that as many Japanese civilians might have died over the course of such an extended war effort, in addition to many thousands on the Allied side), the U.S. felt like we had no choice but to show the Japanese population (particularly the civilian population), in no uncertain terms, that we COULD...and that we WOULD win that war. Because Hirohito certainly wasn't telling them that.
By 1945, Japan was a spent power, with the army in ruins, the economy bankrupt. Let's say it was left alone (AKA not conquered) - maybe with economic sanctions imposed. Japan would have been in no position/shape to threaten someone else - then and (if we assume the american help that followed after Japan's conquest didn't exist), for a long time to come.
But, of course, it would have still been there. And one could say that in ~50 years of so, there was a chance of it regaining its economic/military proeminence, while retaining its aggressive mindset (of course, such long term predictions are inherently unreliable).
Okay. First of all, in a war of this magnitude, involving this many battles fought all over the Pacific.... against THIS enemy, there was NO WAY Truman could have simply 'walked away'. Do you SERIOUSLY think the US population would have accepted anything LESS than unconditional surrender from the only country who has ever attacked us on our own soil? And at that, in such a stunning display as Pearl Harbor was...with such a huge body count? Shoot...even 60+ years later, the photos of the carnage that took place at Pearl Harbor shock the SHIT out of ME - a person who was not even alive at the time, and lost no husband, brother, father, cousin, or neighbor. "Walking away" without a surrender would have been political suicide for Truman. That's pretty much a no-brainer, to the point I'm actually surprised you even suggested it. The US population would have NEVER accepted "Well, those wacky Japanese won't surrender...but we got 'em pretty bad, so we'll just walk away and call it good." NO WAY that would have 'flown'. No way.
Where do you live, by the way? Because even 60+ years later, the emotion surrounding Pearl Harbor is still VERY high, for Americans. The fact that you would attempt a case for 'walking away', makes me think you might not be an American. And If you are, you are CERTAINLY the first American I have ever met to suggest such action.
Well, what were the options to conquer Japan in 1945?
A land invasion with massive casualties would be one of them - and not a very inspired one.
The atom bomb gave the Allies...options.
Foe example - the Allies could have first atom bombed mount Fuji or a military base, "to show the Japanese population (particularly the civilian population), in no uncertain terms, that we COULD".
The military base 'option' I addressed earlier, so I won't circle back on that. As for Mt Fuji....do you realize the place that mountain holds in the spiritual values of the Japanese? I'm guessing not...because if you knew and understood very much about Japanese culture, you would know that that would likely have been a bigger affront to the Japanese than anything else. It wouldn't have terrorized them with fear - it would have filled them with unimaginable and unquenchable rage. Mt Fuji is kind of considered to be sort of an abode of the gods or whatever...CERTAINLY regarded as outside the realm of mere 'human' conflict. Talk about GENOCIDE! Blowing up Mt Fuji, even if not a single human soul died, would have been considered to be MUCH more an act of genocide than would have been bombing Hiroshima. In fact, I would argue that it would have been the single largest act of CULTURAL genocide we could have inflicted on that country. And what are a people without their culture? Without a distinct culture, I'm not even sure there can BE true genocide, in a way. Skin color, after all, is hardly the only indicator of a unique race.
Most countries understand this sentiment. It's why, in the European Theater, certain cities, historic sites, and religious landmarks where considered 'off limits'. In Japan, the city of Kyoto (in case you are unaware, a city filled with Buddhist and Shinto Temples and Shrines) was considered 'off limits'...but whether it was on any 'list' or not, Mt. Fuji would have fallen into that category too. Going after such targets is the equivalent of committing cultural genocide. And in my mind, knowing what I know about the Japanese, is utterly unthinkable.
USA was able to build an atom bomb every 3 months in 1945 - there were enough of them for the Aliies to afford such a warning.
As for "and that we WOULD to win that war" - if need be, that could come later, after the japanese were given a chance to surrender.
But they HAD been given a chance to surrender. You said it yourself - they were practically on their knees. And still unwilling to surrender. Instead of surrender, we were getting Kamikaze pilots running planes into ships and such - at that time, an act that was completely incomprehensible to the us. And REMAINED incomprehensible to us for a very long time - at least until about 8:45:59 am on the morning of September 11, 2001.
You REALLY do not understand much about Japanese culture, do you? Throughout your arguments, you seem to be making the mistake of thinking that their values are the same as ours, that their communal way of thinking (and in Japan, there IS a communal way of thinking - it is NOT the most individualistic country on earth) would net the same conclusion and following action plan as our, more individualistic, way of thinking.
But trust me - blowing up Mt Fuji? Not the best of plans, if the objective was to facilitate surrender.
You think Americans are the big guns, when it comes to holding our own culture in the highest regard and defending it at all costs?

Oh my...we are the bush leagues, compared to the Japanese - who have a very proud culture that is thousands of years old and that is much more holistic than ours is - involving WAY more than the right to shoot for a big bank account so that we can build monuments to ourselves. Our 'culture', in fact, is defined by our complete LACK of homogeneous culture, and is characterized by a minimal regard for the well-being of 'the group' as opposed to the individual. In Japan, it's the exact opposite - it's all ABOUT being homogeneous...and it's all about the group. And 'the group' includes every Japanese person who ever lived. *We* can barely resist dishonoring OURSELVES, most of the time, it seems. In Japan, they worry about dishonoring ancestors who are long dead. With such massive differences at the foundation level, we cannot assume that the value they place on culture, as opposed to individual human life, is remotely the same as ours.
The Allies could even have used atom bombs of smaller destructive strenght to destroy anything that resembled military bases in Japan, effectively destroying any meaningful japanese resistance to an eventual invasion (gangs made out of civilians with small weapons not counting as meaningful resistance).
Once again...hitting military targets was not working...and was not GOING to work. Such actions are expected in war time...and it would have taken a lot more than hitting a bunch of military targets to accomplish the unthinkable and
successfully turn the Japanese people against their own emperor.
To get them to do what for them, was an unspeakable act, we had to commit an unspeakable act.
I don't think that anyone is saying that dropping two atomic bombs was a wonderful plan that we should all be comfortable with. Because we SHOULDN'T be comfortable with it.
But what I think we CAN be comfortable with is idea that Truman & Co. honestly believed it was the best choice they had among an array of really BAD options. Most estimates I have seen place dropping those bombs in a place of LESS overall loss of life (including Japanese civilian life) than if we had allowed the war to drag on and on via opting for any of the REALISTIC alternatives (the chief one being a ground assault on mainland Japan).
Sometimes, there are no good options - only varying degrees of 'horrendous' options. And I think we
can be comfortable that this was one of those times.