I expect that historians will mostly remember it as part of the "War against Terror" which along with Iraq was the two principal distractions which most contributed to keeping the United States from dealing with dealing with the peak oil energy crisis in time to avoid the second great depression.

I'm not sure that the atomic bomb is a particularly relevant comparison.  The use of the atomic bomb was not controversial at the time and has become so only in hindsight.  The government use of torture is controversial now and will be almost universally condemned in the future, at least until the time comes around when it is used as a precedent.  This will place it historically somewhere between the Japanese Internment and the Alien and Sedition Acts.

Looking at some the court decisions, particularly in the Padilla case, you really have to go back to some of the cases involving the right of slaves to contest their status as slaves to find as bad or worse abridgments of constitutional rights allowed by the courts.

Torture in POW camps really isn't all that unusual, but the U.S. likes to thinks of itself as better than other countries, and that's hard to do with the top government officials openly advocating torture.  I can't come up with another example of U.S. officials ever being stupid enough to advocate torture openly before, though certainly sponsoring it by proxy hasn't been unusual, and on occasion the military has looked the other way well up the chain of command.

There are some commonly held misconceptions about Guantanamo.  Real torture at Guantanamo, while not especially uncommon is more the exception than the rule.  The government likes to talk of the prisoners there as the "worst of the worst,", but if you read a bit of the detainee status hearings materials, it becomes clear that the majority of the people there are ordinary Taliban foot soldiers, with a scattering of people who regard themselves as Jihadis, as well as a scattering of people who were just in the wrong place at the wrong time or were turned in by an anonymous informant with a grudge against them.  Taliban soldiers were the official army of a government, and are legitimate prisoners of war but are not terrorists, and never took orders from Osama bin-Laden or other terrorist groups.

The government tries to give the impression that the people held in Guantanamo are the subject of intense investigation of terror cells, and while this is true in a few cases, reading the detainee status hearing transcripts makes it clear that the majority of people in Guantanamo have just been dumped there and forgotten, without doing any of investigative work at all on them.  Evidence against them, including that which they were carrying when captured has usually been lost.  In most cases, the most cursory investigation of them reveals that there never was any reason to believe them to be part of a terrorist organization.  The political desire to equate the Taliban with Al-Quaida doesn't allow differentation between the two, and this means that the military labels them as "enemy combatants" or not, and doesn't differentiate them into "Taliban prisoners of war" and "terrorists and terrorist supporters".  Partly as a result of conflating these two groups, even in those cases where it is clear that the prisoner supports terrorist actions against the U.S., usually no investigation has been undertaken to use their capture to track down other potential terrorists.

Guantanamo has been the showcase jail of the C.I.A. secret jail system for years, and this has somewhat reduced prisoner abuses there.  Conditions in the other C.I.A. jails are considerably worse.

I see it as more likely than not that high U.S. officials will be indicted for war crimes in Europe, but of course popular sentiment and elections are hard to predict.  We already have C.I.A. Agents on trial for their official duties.

Your link about the use of the atomic bomb is interesting, but it dodges questions about the choice to demand unconditional surrender.  I tend to go along with the camp which believes that the use of the atomic bomb was not necessary because even before it was used the Japanese were willing to surrender on the terms eventually offered them, even though they were not willing to surrender "unconditionally".   On the other hand, I believe that once the decision to demand unconditional surrender was made, its use became the correct decision from the U.S. point of view.

One thing that people often don't keep in mind about the Nagasaki bomb is that that was the last bomb that the U.S. had ready, and that they were producing only one every  2-3 months, so that they were essentially trying to bluff that they had an unlimited number available by showing that they didn't mind using two of them in a short time period.

I reject the argument about scaring Russia.  The hardest part about building a nuclear bomb is simply believing that it can be done.  Germany were well ahead of the U.S. in constructing one before they scuttled their project as unrealistic.  Of course there's still some difficulty in getting a high yield explosion instead of a "fizzle" like the North Korea test, but once a technologically sophisticated country like the U.S.S.R. seriously sets to work building a bomb, they're going to succeed, so the best strategy, (assuming that you don't know that the secret is already out, which it was) would be to keep it secret that you have one at least until you really needed to threaten someone.