It depends on how it got there, but if it was host-free then it wasn't a virus. Probably an IE Exploit or packed with something else downloadable. Anyway, the reason it wouldn't be a virus is because it probably lived outside another process. Just because its payload was aggressive and it got there without consent does not mean it was a virus. It must become a part of another process in order to become a virus. Just like in nature a virus injects cells with parts of its own DNA to infect the cell (AIDS), the same is with computers and what we know as a computer virus. Keeping in mind that there were once boot sector viruses (a little different than what we are use to today) but that kind of died out after NTFS because of the way it boots and its added security on the hdd.A little off topic, but I have heard of a virus that was helpful before. iirc it installed itself silently on a users computer to attempt to undo and fix their computer by getting rid of another (harmful) virus automatically. I dont remember the name atm, I'll need to search for it again..
I think what you are talking about is actually a windowless process installed by means of exploit or it was packed with something else by a group of virus writers having a fight. I assume it just went around tagging clean files and removing or cleaning bad files infected by the other virus. Unless it also wrote itself to the files then it was not a virus, even after tagging the file IMHO. Normally viruses are very bad and are often quite harmful rather than helpful. Plus, like I said they are boring to write. Now something cool to write is packet sniffers (WinPcap), switch sniffers (ARP Poisoning); things involving reconnaissance. Both challenging and quite interesting. haha