A U3 drive might be able to do that. You'd have to get the virtual disk to run before the flash drive mounts and I'm not sure if that's possible.
Or carrying 2 flash drives. It'd be like U3 but there's no chance of the other drive mounting first. The first one has anti-infection and the second one has your data. Make the first one read-only if you can (use a U3, leave the rest of the drive blank), run the program, then plug in your other drive.