The article I linked tells how Rodney P. Quarles Jr. had access to the State Dept. records. But it is possible that all his queries were meant to cover up the queries into the VIPs (in other words bury a few queries with hundreds).
Imo there was a scam going on, but I fail to see how these low-level employees were able to gain access to the VIP passport details. Security surely couldn't be that poor?