<< He can boot with a DOS floppy whenever he likes. >>
That may work, but what if the app needs to access data on the hard disk? If the drives are formatted in NTFS this won't work. You won't be able to read/write to anything. There is NTFS DOS, but u don't wanna give him that and it's probably best not to use FAT 32 so u can lock things down using the NTFS permissions.
EDIT: If the program can infact be run from a dos floppy then i suppose you could partition a fat 16 or 32 section of the hard drive for use with that app. There would be no security on anything in this partition however.
or
What if the app was run remotely? You could handle the app itself from a 98 machine, or whatever it takes to run, then the drive could be mapped and he'd be able to use it remotely in 2k. I can't see why running it off a 98 machien from 2k wouldn't work. This way, u'd also be able to secure the machine yourself and everyone would still be using 2k.
Ha, who'd ever think a 98 machine would serve to NT!