Delete photos from iPhoto and delete originals that aren’t in the iPhoto folder

As you don't seem to use the iPhoto library at all, you should use Image Capture instead. It allows you to put your picture directly in a given folder.

You can also create a "transfer module" with automator which can be set to run after an import using Image Capture with imported pictures as input. Thanks to this, you can create an automator process to arrange them in folder as you want.

Image Capture is also scriptable with AppleScript, you might want to take a look at its dictionary if the GUI or Automator don't provide enough flexibility for you.

If you want your pictures both in iPhoto and in your folder, you can configure the automator process to add them in iPhoto once imported in your folder with Image Capture. Lots of workflow are possible, it depends and what you exactly want to achieve.

It is a bad idea to try to manually modify the folder structure inside the iPhoto library, as you seem to want to do.

The best way is to follow Apple's instructions for rebuilding the iPhoto library.

However, this is usually only used as a repair procedure if iPhoto is malfunctioning.

You can try this, but make sure you have a complete backup of your iPhoto library before you start the rebuilding procedure.

Also, realize that iPhoto has an internal Trash that is separate from Mac OS X's Trash. If you have deleted hundreds of photos over the years, and never emptied the iPhoto Trash, those photos will still be in there and taking up space in the file structure.