Ipods are a pain on Linux because of apple's updates. The truth is that it works quite well with stuff like gtkpod/banshee as long as you
never plug it into itunes. Itunes messes up and updates the library and creates havock.
I would try update/sync your iStuff over wifi if that is possible, i mean plugging things in to sync is so Palm/PDA world ;-) Then again my smartphone runs ssh+rsync so it makes it a bit easier!
I've got a shuffle which never got plugged into itunes, plugged it in once (apparently there was an update that improved battery life or something), and bahm stopped working in Linux. Thankfully fixed with a full revert - formatted the disk from linux and made amarok initialise it again
Good luck with the wife, my girlfriend is on Arch Linux and doesn't seem to mind the KDE4 desktop. She had Vista before which more than anything was super slow on her cheap Acer laptop.