I've actually run into this problem as well, here is my expereience with it.
iDVD6 does not recognize anamorphic as 16x9. You can do all the correct settings and it will still display the video as 4:3. If you give it video in a 16x9 format, i.e HDV, it shows up as 16x9 on your preview. However, the anamorphic pixel aspect ratio does come across on the dvd so if you watch it on a 16x9 tv, it shows up properly. BUT if you play anamorphic on a laptop, it shows up as 4:3 while HDV shows up as 16x9.
One thing i did that took forever was to convert the anamorphic 480 footage to a 16x9 equivalent(960x540) and that worked decently. But this was just to send a client a rufcut test dvd. Otherwise, the best way to handle anamorphic is through DVDSP