i dont think so. ever thought about switching to eclipse or netbeans ?

It did occur to me... but deadlines are tight right now, and processing for eclipse has a certain learning curve I understand.  Is it worth it, do you think?

You cannot use sub-directories, alas.
But at least, you can split the code in several .pde files (and/or .java ones, eg. if you have interfaces or similar pure Java files).
I did that for a maze generation sketch which I plan to announce after improvnig it a bit more, but you can already have a look at http://bazaar.launchpad.net/~philho/+junk/Processing/files/head:/MazeGeneration/ if you look for inspiration.
It isn't as big as your sketch, though.

Another solution (not usable if you lack of time...) might be to put part of the code in a library...

take a look at this site, http://code.google.com/p/processing/wiki/LibraryOverview
it also tells you another alternative way. by putting code in the code folder