And apparently the Soviets, who had essentially no capability to launch a amphibious invasion, were a serious threat to the Japanese home islands. You know, compared to the country which had just launched the most ambitious amphibious operation in history.
The Japanese government at the time was prone to ultra-nationalist factions and extreme instability, and the problem with the idea that they would surrender just because the Soviets had closed off one of their options was that, although any individual leader might well know that their situation was untenable, anyone who acknowledged this would be prone to a coup by nationalist junior officers. The incentive structures of Japanese military leaders was such that it would be extremely difficult to justify ending the war. Otherwise, they would have de-escalated with China in the first place, or at the very least following the US embargo.
I'm being far less fair than I should be, but so is the article itself - the story it presents is plausible revisionism and is taken seriously by historians, but it is revisionism nonetheless; there is a reason historical consensus is historical consensus, and saying that "there is a real resistance to looking at the facts" ignores this. The story that the Soviets caused the surrender is perfectly plausible, but so is the story that the bombs did. My own feeling is that the article is written in bad faith.
As an aside, the idea that nuclear weapons were widely considered horrifying at the time is very much an anachronism. Nobody really understood the consequences at the time; to give you an idea, Operation Downfall planned to use nuclear weapons as an opener and then march US troops into the blast zone after 48 hours.