if you miss a leg of your flight , then the following legs are automatically cancelled , then sometimes its worth paying
but OP didn't a miss leg (or no-showed)! The connection-time was insufficient. This is Aeroflot and Russia.
What do you think will happen if you refuse to pay the rebooking fee? As most travellers need a visa to enter Russia, this problem becomes the problem of the Russian border guards (border service FSB). And I do not think they will like this kind of game Aeroflot playing with their passengers.