I'm not really very deep technically on software updates, but a question about using ITMU with Configurarion Manager came up and so I went to the source of all software updates knowledge: Doug Eby, the software updates writer for Configuration Manager, and he has enlightened me/us about this subject:
ITMU is only for SMS 2003 clients in the hierarchy. You have to upgrade to the Configuration Manager version of the ITMU on the central site in order to create software update deployments for SMS 2003 clients assigned to Configuration Manager sites (or SMS 2003 clients assigned to SMS 2003 child sites of the Configuration Manager site). When all SMS 2003 clients have been upgraded to the ConfigMgr client, you can remove ITMU from the environment.
In other words, if you're using ITMU in a Configuration Manager site to support assigned SMS 2003 clients, you'll need to install, configure, and synchronize the active software update point before upgrading clients--the ConfigMgr software updates client agent ignores the results it if the scan source is ITMU. After the software updates client agent is installed on upgraded clients it will scan for software updates compliance and then you can deploy software updates to them using the ConfigMgr software updates methods.
During the upgrade, ITMU should automatically be upgraded if it is detected AND if there are no other installations of ITMU higher in the hierarchy. Once the upgrade completes, synchronization will automatically occur, and then the client will be updated with the new scan package. So, unless the upgrade fails, you shouldn't have to do anything to upgrade the ITMU components.
So, to me it looks like if you're using ITMU to patch clients in an SMS 2003 site, and you're going to upgrade the site to Configuration Manager, then you need to leave ITMU installed during the upgrade and allow the previous ITMU installation/client scan tools to be upgraded to the ConfigMgr ITMU version. Next, install and configure WSUS/active software update point before beginning the client upgrade process to maintain software update compliance.
Hope this helps!