If you don't want to actually use iPhoto as your photo manager, then don't.
No. iPhoto does not keep your library in a typical folder structure. So what? If you're using iPhoto, there's no reason to ever go in there. If you want to export a photo for use in something else, just export it from iPhoto.
Personally, I'm glad iPhoto manages the files in whatever way it wants. I can't keep track of hundreds of folders with thousands of files all named "DSC03271.jpg" anyway. I want a visual manager for the visual medium of photos. To me (ymmv) it just makes sense.
Do you feel the need to rip open your car's engine "just to peek around" from time to time too?