Most viruses kill the host cell, or at least render it incapable of performing its normal function, so if most of the cells of a type are infected you are in trouble anyway.
Ideally a way to excise the viral code from the cell would be found. DRACO basically activates the destructor on a cell and ends the entire cell, even if it is still serving the body.
I also recall that our chromsomes contain the genomes of viruses that have been overcome over the span of our species life on this planet. Whether these fragments would get affected is something I'm curious about.