You may want to try changing Setup -> Email Administration -> Deliverability -> Access level = "No Access" during your data migration/load activities. Naturally you should test this in a SB to ensure it meets your needs.

Unsure about how to prevent the Product Owner from receiving updates to user stores other than the Notification Level = "Bread & Butter" above. I do see a field called "Email On Save" (agf_Email_On_Save__c). You may want to see if that field could be potentially leveraged to suppress story updates to certain Product Managers that don't want to know about what's happening to their User Stories.

I'm a fairly new Admin of Agile Accelerator myself. Perhaps one of the more seasoned veterans will have a nicer way to prevent emails to certain production managers.