You can definitely use iTunes without having it copy the music into it's own directories. You just uncheck the option to "copy files to Library" somewhere in the Preferences.

You could run a daapd server on the Linux box, which would cause the Linux box to appear to iTunes to be just another iTunes computer on the network with all of your music already on it. However, I don't think you can get the iPod to sync with music shared with daap.

It sounds like your best bet is to just get iTunes to build it's library out of your files without copying them over, and then arrange things however you want to sync them to the iPod. Only caveats are that any changes you make to the tags in iTunes aren't just local to it's database; they'll propagate to your files (which may be good or bad in your case). Additionally, other metadata gets written to your files as well, like the "Soundcheck" volume normalizing data.

There may be some other third party product that works better for what you want, but when it comes to iPod, I only know iTunes personally.