I am unexpectedly taking over for the previous administrator of our TFS system who left the company rather abruptly. I was made an admin of TFS and on the TFS application s
This worked for me on TFS 2010. basically there's a stored procedure that removes subscriptions in the TFS database.
tfs_yourprojectname.tbl_EventSubscription and right click => select top 1000prc_UnsubscribeEvent in the object explorer, right click and select "execute stored procedure". enter the value of the id column in the event subscription table for the alert you would like to remove.