-Removed-The difference is that it's a single weapon. In a bomber stream attack each bomb was either an incendiary or a 2,000 lb high explosive. There's a basic problem in the rules of war of going for an attack of that type of a city called distinction. Basically, military forces cannot deliberately target civilians and their attack should be against a military target. About the same number of people were killed in the fire bombing of Tokyo (at least 80,000) as Hiroshima (90,000) and more than in Nagasaki (39,000) [1]. So a conventional attack can kill about as many people as a nuclear one.
However, the question is about the morality of the weapon. Towards the end of the war there was a Tallboy attack on a tunnel near Saumur which successfully collapsed the tunnel [2]. The Germans hastily excavated it, but the attack delayed an SS panzer division from reinforcing Normandy. Anyone in the immediate vicinity of the blast or in the tunnel would be in trouble, but the nearby town was unaffected. Had they been using a Fat Man device (not that they were available then) then it would have gone badly for the town. Simply put a Tall Boy bomb could be used in such a way that it's use does not affect civilians not in the immediate vicinity of the target. With atomic weapons that is much harder.
I think it's possible to select targets which minimise the effect of atomic weapons use on the civilian population of a country being attacked. However, the nature of the attack makes significant levels of collateral inevitable. So it's on these criteria that nuclear weapons should be judged. Carpet bombing is an attack profile, not a weapon.
[1] These are the low end estimates from the relevant Wikipedia pages:
https://en.wikipedia.org/wiki/Bombing_of_Tokyo
https://en.wikipedia.org/wiki/Atomic_bombings_of_Hiroshima_and_Nagasaki
[2] https://en.wikipedia.org/wiki/Saumur#World_War_II
