Though you can't undo iTunes's folder organization, I believe I've found a way to defeat iTunes.
I used Automator to (a) find all files in the iTunes Music folder which had an extension of m4a (don't use a period before the "m"); and (b) copy all found files into a different directory (if you're feeling confident you can have Automator move the found files rather than copy them).
I have 45,000 tracks so I set it up last night and when I got up this morning, all the tracks were moved over.
The next step is to highlight all songs in the iTunes application and delete the songs (but NOT the files).
Next, you go into iTunes preferences and uncheck the "Let iTunes organize your collection" choice.
The final step is to add the songs in the new folder into iTunes. My report from home is that all the songs came back in, with full metadata, sortable by any field for which there's metadata.
This was relatively easy, and let me, if not undo iTunes organization, at least explode the entire structure and start again.