I think that you have bigger problems than you think. What about physical security?

Hey if you can't trust the users not to mess with it, you shouldn't be letting them anywhere near it?

If they have physical access then they could use boot disks/CDs or whatever to crack your system?

And when your bosses will not allow amendments, it does not sound if they have clearly defined their objectives, or the "rules of engagement".

I don't know the politics, but I really think that you need to get this sorted out...........why did the original developer leave before the job was completed?

just a few thoughts