Remember, Stalin didn't go in for executions; he preferred slave labor. Deaths in the GULAG -- which could be as high as in the non-death-camp Nazi concentration camps, or higher -- should be counted as well as executions. (Remember how part of Stalin's price for peace with Japan was 300,000 Japanese slaves, none of whom ever returned to Japan after the war.)
Also, some deaths in the war should be attributed to Stalin -- at the very least, deaths in the punishment brigades. If you force someone to march through a minefield, and he hits a mine and dies, it's your fault.
That's a war, Nazi Germany attacked USSR, people had to fight them, Stalin is not a field officer to force solders to march through a minefield, people die in a war, I don't think you are right here equating people who died fighting for their country with those who were executed for whatever reason.
Most of those Japanese POWs who survived the winter of 1945 / 46 had been repatriated by 1956, with mediation by the Red Cross.
Furthermore:
In 2005, the Russian government provided the Japanese Ministry of Health and Welfare microfilms of personal information of 40,940 Japanese POWs who had died during their detention.
Still horrific but less than 10% of the total number.
There is a fascinating history of those who returned to Japan but couldn't fit-in again due to Soviet indoctrination.