I'm pretty sure you can do what you are asking for with
foobar2000: Components Repository - iPod manager (if you are willing to make a switch to foobar)
I have had instances where my iPod corrupted on me though (when I used mediamonkey), and nothing is better for that than iTunes unfortunately. If you are afraid of it leaving crap behind, you can use an advanced uninstaller (it scans for remnants in your files and registry).