Can I tell iPhoto to store photos in one directory within the library?
No. iPhoto does not allow you to dictate the internal storage scheme. However, the export function does have an option to export the original file, so you can avoid the re sampling and/or format conversion if that is enough to stick with what you have. Additionally, Aperture and iPhoto can use the same storage, so you could get aperture and do the following;


convert the storage of any photos you want to folders and then save the library. 
continue to use iPhoto for convenient tasks and iPhoto will work with the aperture store locations. 
do all imports in aperture when you want the originals stored in specific folders. 


You can use Lightroom, PhotoMechanic or Aperture which all allow whatever folder based storage of photos you prefer.