Most Linux apps read the database first, the whole wiping and Syncing in
iTunes is a DRM measure designed to prevent you from dumping songs you
didn't buy off of someone else's iPod.
I'd connect it and find out, you can always restore from iTunes if you have
to. However, iTunes won't work if you use something else to sync with it,
so if you went back to iTunes it would require a full restore.
Be careful also, sometimes the latest and greatest isn't supported yet in
Linux, but your experience may vary in this case, iPod's are pretty popular.