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:
- disableCheckForUpdates
- disableAutomaticDeviceSync
- disableGetAlbumArtwork
- disablePlugins
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.
Managing OS X 
I found one small side effect to running:
defaults write com.apple.iTunes disableCheckForUpdates -bool YES
After I did this, the Update and Restore buttons in the iPhone preferences in iTunes were grayed out. Pretty strange that this plist file would control that, but it does. After I ran this:
defaults write com.apple.iTunes disableCheckForUpdates -bool NO
I restarted iTunes, and those buttons were available again. Very odd that this flag would prevent you from restoring your iPhone?
@ Jeff – yes, since this key/value pair disables checking for updates, this affects iPhones–and iPhone Restore functions, consequently.
The Restore function is likely closely tied to checking for updates.
I can confirm the same observations you’ve made, and that changing the end of defaults command to -bool NO permits Check for Updates and Restore functions on iPhone.
In each case the preference does not take effect until relaunching.
This also affects iPhone app update checking, as well as iTunes update checking and iPhone update/restoring. Your list of iPhone apps will still be available, but the “Check for Updates” and “X Updates Available” will be greyed out.