Due to the nature of how Shogun 2 and Fall of the Samurai are integrated in multiplayer unfortunately, even without Steam, such a large patch when re-installing the game from disk is necessary. If you had have been re-installing the game from a recent working backup of the game's data then there either wouldn't have been a patch needed at all, or only a small patch would need to be applied if any updates had taken place since the game's data was backed up. Company of Heroes can have the same issue and that isn't even a Steamworks game.
Just keeping a simple copy and paste of the Shogun 2 directory somewhere safe to paste back in the Steam folder if reinstalling does the job, though I use the Steam Backup tool personally since it is fairly easy to use.