The americans produced very few atomic bombs initially, and the weapon had never even been tested by the time operation unthinkable was supposed to begin. Not only that, but they have no means to deliver an atomic bomb in europe, all the nuclear capable b-29s and personal are on the other side of the world and it is going to take months for them and their support personal to relocate to bases in England.

That b-29 is going to have to penetrate soviet airspace and the Red Airforce defenses. The western allies will not have air supremacy initially and securing air supremacy like that had against germany or japan will take months of even years of bloody fighting. Moscow is at the very limit of the B-29s range and other prominent soviet cities in western russia like lenningrad, kiev, or minsk are all pretty much rubble from fighting between 41-44 so dropping an atomic bomb on them isn't going to do much.