It would be interesting to know how the cost of the fan + electricity + the cooling effect of air movement compares to just leaving it alone.
Any time you get a big temperature differential like that, the rate of heat loss goes way up, particularly in Winter. Not only do you slow down the heat loss in the atrium when you push it back down, but you are recycling the heat back down to the living spaces. The temperature really goes high up there when the wood stove is in operation. I think of the heat generated during that time as FREE, so it supports the fan, financially speaking.
The purpose of the atrium is actually to create a powerful cooling tower through stack effect so the passive solar doesn't get too hot in the Summer.