Your problem was the main reason why I uninstalled iTunes and downloaded a program called "4VideoSoft iPod Manager" to manage files in my iPod. The only sad thing is that it removes all the album art, and the added songs don't show up in your total songs/vidoes count (Read the word "COUNT", you can still access those files in your iPod).
So I suggest you download it. Its not for free, so you have to pay for it. But you can freely use it for 15 days, I think.
And yes its legal and does no screw up your iPod. I have had no technical problems with it apart from the bug I explained before.
[Edited by HonestGamer, 7/8/2010 8:01:56 AM]
Why would you pay for something you can get for free??