Você precisa verificar as notas da versão de cada versão, mas as instruções de atualização para a versão 2.0 estão aqui:
Os dois últimos marcadores abordam especificamente sua pergunta:
To upgrade a replica set. Upgrade the secondaries first one at a time, then stepDown the primary and upgrade the primary. Using the stepDown command is better than simply shutting it down since the failover will happen quicker. To avoid losing the last few updates on failover you can temporarily halt your application (failover should take less than 10 seconds) or change your application code to confirm that each update reaches multiple servers. Note, after upgrading to 2.0 you can use the shutdown command to shutdown the primary without losing any safe updates.
To upgrade a sharded cluster. Upgrade config servers one at a time, in any order. Since config servers use two phase commit, shard configuration metadata updates will halt until all are up and running. mongos routers can be upgraded in any order.
O tempo de inatividade é mínimo, levando apenas o tempo para o Replica Set confirmar que o stepDown ocorreu e que a eleição / promoção ocorrerá.