Maybe in this scenario Luftwaffe bomb Moscow so heavely that Stalin tries to slip out of Moscow pretending to be a Sovjet Civilian?
Does the top dogs of the USSR still fight on?
We'll leave aside the question of why Stalin has decided to go for a country ramble through Operation Typhoon.
I for one question the effect this would have on Russian morale. Sure, there was a cult of personality, but the Russian people were by no means fighting only because Stalin said to: they were fighting because if they didn't, the Russian nation was well and truly fucked. That's still the case, and given the precariouss situation the Soviet bigwigs (I don't know who was in and out of favour at the time) will probably save any murderous power-struggles they plan to have till after the war.
The effect of removing Stalin's strategic, ah, "input" would be interesting, though.
(they all knew Stalin was a just man; a terrifying man, but a man nonetheless)
Actually if Stalin was captured there would be a massive struggle for power in the Soviet leadership. The head of the Secret Police would probably attempt to seize power but there would be a fight and the Russian military would probably get involved. This would offer the Germans a great chance to win the war.
To be honest, I think Beria, Molotov, or whoever was suddenly running the show would immediatly showcase a Stalin body double to counter German claims and make them look like liars. When the Soviets eventually win the war and assuming they capture the POW Stalin, they will welcome him back to the victorious side with a bullet through the brain.
Surely if Stalin was captured he'd be brought to Berlin to engage in Thunderdome style gladiatorial single combat with Hitler to decide the future of Europe?