Try using a Virtual machine for the OS/application that needs this level of access. Another mechanism could be Citrix or Terminal server. You can look at some of these resources also for suggestions:
There are utilities/software out there that can temporarily elevate authority while the application is running. We use a VB shell around a couple of applications to elevate authority and it seems to work well.
the best way to verify that the Active Directory is being backed up is to examine your backup logs, and ensure that the system state has been included. I would also recommend testing your backups periodically to make sure that the Active Directory can be restored. You can install Windows Server onto a cheap PC can use that PC as a way of testing your backups so long as it is not connected to the network.
As for the DOS programs, I would recommend running them in a virtual machine environment, or hosting them through a terminal service session.