Disable "check for updates" iTunes AND allow update iPad iPhone

In an enterprise environment we followed http://support.apple.com/kb/HT2102 to disable the "check for updates" in iTunes, although this is preventing users from updating thier iPad and iPhone devices as well.
How would we manage the Windows computer software (disable check for updates) but allow users to manage (update) thier own portable devices that require iTunes to update?

No.  For now we have decided to perform the default install for our users with specific instructions not to update when Apple informs them of an update.  When they see the pop up notification of an Apple update, they are to open the SCCM (SMS) "Run Advertised Programs" where we have packaged the new version to install with Admin rights.

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