Delete provisioning profile from Xcode 5
In the Xcode Preferences, go to Accounts, then go to your apple ID, then click "View Details"Click the provisioning profile which you would like to delete, then press the "delete" key ONCE. Then click the refresh icon for manually update the list(pretty counterintuitive...).
Using this method I was able to delete all but one copy of the same provisioning profile, after which the delete does nothing.