Wasn't that decision made prior to 1939? (1939 or later POD specified)
True. But it could also probably be undone if there was some reason to do it or even if they just wanted to. Estonia and Finland being integrated or in the Soviet orbit eliminates any reason for it not to be the case. The only issue is that the Moscow/Saint Petersburg divide is a divide based on stances on social issues the later you get. Saint Petereburg is Liberal, accepting, and in many other ways western, Moscow is conservative and properly Russian. Moving to Saint Petersburg would symbolize a major political shift away from Stalinism. So Krusvhev could maybe even justify the shift on Destalinization grounds. (Overall, it would provide decent justification for a soft purge of bureaucrats disagreeing with the new person in charge).