Workgroup Manager/MCX supports managing some iTunes preferences if you use the Preference Details and add the Managed Client preference managements.
It turns out there are a few more things you can manage if you look here.
These additional items include:
and more. These also seem to work as regular default keys. For example:
defaults write com.apple.iTunes disableCheckForUpdates -bool YES
turns off and disables automatic checking for updates. You might want to do that if you manage installation of iTunes updates yourself.