It wasn't so much a "Demolish RFID (physically)" spell as much as a "Nullify RFID", destroying the data therein spell. It would not be able to differentiate between stealth RFIDs and normal RFIDs, but it could work just as suggested, creating an area, emp-type emanation.
All you'd have to do is cast it after creating the object, so that destroying the desirable RFIDs in the feedstock wouldn't be a problem.