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The problem is that a virus isn't really "alive" to kill, it's just bits of DNA that "reprogram" living cells to reproduce itself. So, we're stuck with trying to block them from entering cells, or trying to block replication once they're in cells.

I have given this quite a bit of thought.
If I understand virii correctly, they attach themselves to cells and then inject their DNA into the cells, which forces the cells to manufacture more of the virus.
If scientists could manufacture a "friendly" virus that would attach itself only to "evil" virii and inject their friendly DNA, then in theory evil virii could be wiped out.
Also, I know that virii can/will attach only to specific types of cells (or locations in the body), so it may be possible to manufacture friendly virii that seek out specific evil virii.