I have to admit, I've just given over to using iPhoto as the direct interface for dealing with my photos. I don't deal with the folder structure at all anymore. I've found creative ways to get photos out (drag and dropping straight iPhoto to folders creates copies, for example) when I need to make change to them, etc.

I definitely understand the annoyance, though. Although I think that it's being done that way to accomodate for larger and larger photo libraries.

There does seem to be a choice of whether or not to copy files to the "iPhoto Library Folder" in prefences, but I'll be honest, I'm not 100% sure on what would happen if you did turn that off. :)