Shame on You
Nope. I think the argument about birds and dinosaurs has moved on to other aspects. Discovery of true dinosaurs with feathers has caused a shift. I doubt anyone is willing to go out on a limb and say feathers evolved independently twice.
Apparently a lot has happened since 1992...
There is a problem with cladistics and viruses: horizontal transfer of genetic information. You have no guarantee of getting a phylogenetic tree. (Technically, it becomes a directed acyclic graph, or dag. Viral heredity can present problems even Cleopatra VII lacked.) XMRV seems destined to break with human conventions in this area also.
Yeah, recombination/pseudotyping can screw up cladistic analyses of retroviruses in particular. Not only XMRV but just about all MLVs seem quite capable of swapping DNA, so the entire "MLV-related virus" population could make for a very weird-looking family tree if the implications of the recent NCI/ WPI work and the Alter study are any indication. It will at least help to have complete viral genomes; just looking at sections of the gag gene won't be enough.