With ADFS infrastructure, you can set the mail attribute of the user account to match the UPN used for login (usually email address). Office will be automatically activated in the background. Geek of All Trades: Office 365 SSO: A Simplified Installation Guide. I'd recommend you have a look at the following guide and see if something is set incorrectly: As far as I know, if ADFS is set correctly and SSO is enabled, users can sign in Office automatically when they log onto Windows and start Office program.
