1) The viruses & malware won't do any harm unless activated (run). So, as long as you know they are there and handle them appropriately you can be safe. Think of this as being a bio-lab that happens to have either Small-pox or Anthrax in their collection.
2) With that in mind, I would consider keeping it but, as long as you document your actions carefully, no one could blame you for exporting everything and deleting the original container and offending file.
3) Again, document everything, but it depends on the container. I don't know about PST (haven't had to deal with that one in this way) but MBOX and its varieties could be easily modified to cut out the offending bits.