I don't think it will work, at least not the default way Remote Desktop mounts local drives and not in the test I just tried.
Remote Desktop mounts the drives as a network share so they no longer look like USB sticks. An exported Opus on a USB stick will only run from the same USB stick. Running it over Remote Desktop is like copying the files off the USB stick and putting them in a network share, then running Opus from that, which won't work.
Remote Desktop can pass through USB devices but it seems to exclude USB drives from that. (I'm connecting from XP SP3 to Vista SP1 so features may vary with other versions of Windows.)
What may work instead is taking your normal Opus install (i.e. on a harddrive not a USB drive) and sharing that folder, then running dopus.exe on the server via that share. I just tried that and it worked, but I tried it on a machine that also had Opus installed normally so it wasn't a complete test.
Edit: Opus needs to register some COM objects to work fully, but only for UAC support (not relevant with Server 2003) and Zip support on 64-bit Windows (might be relevant but if you're using 32-bit Server 2003 then won't be an issue). So using a normal install over a network share should work, at least in theory.