1 - There is an automated stop to the process. It doesn't continue to move through the system, so the preservation environment remains clean. You go back to the source and request to get another copy that is clean.
2 - It may be possible to view this material on a throw away computer to see what is happening. From this experience, you can decide better what to do.
3 - Is the virus a critical part of the environment that you want to maintain? A computer science researcher who studies viruses will presumably have viruses on his machine. In preserving his work environment, do you want to keep his copies? Store them in a secured partition? Are there other things you can do? Especially if the viruses are older, are they actually dangerous anymore?