That may be my fault, as I don't know much about Citrix...
When you say the registry is a mess, is it the FPMXL* entries that worry you or the Office entries? What does the registry look like when you uninstall IBP? Because what the EPM registry cleaner does is it cleans up any FPMXL* entries that are left over after the uninstall. It will not clean up anything else and it must not be run while IBP is installed. If that is what you feel you need, I'm happy to send the file to you.
And yes, I was expecting the end users to have access to the AddinManager on their Citrix window - they obviously have access to the IBP installation folder, since they can run the add-in. Can they not access that folder in the Windows Explorer and run it? Maybe with your guidance and just to see if it helps?