Leaving aside, for the moment, the question of whether or not a virus is 'life' -- this question would apply to a bacterial disease as well -- how is this any different than the attempts in the last century to eradicate the North American wolf? They were dangerous (and quite inconvenient) to humans. Thankfully (to some...) we failed, and many people are happy they are returning. The reasons we wanted them gone haven't changed (although hardly as much an issue with the hugely reduced numbers).
If it's not OK to eradicate a species that looks like the family dog, what about if they were squirrel-sized? Insects? Where's the line, exactly, where we say 'OK, on this side, it's good and right to completely remove this species from existence, but on the other side of the line, it's a 'protected species' to be preserved, and we just control it? One could argue that wolves served a purpose in the ecosystem by controlling deer and other game population -- but honestly, we will never allow the grey wolf population to grow to a number to have any real effect on that anymore.
Not really taking a side on whether or not to eliminate the stocks we have of smallpox, but I feel like there certainly is an ethical question in whether or not it's OK to do so.
(As a side note, I think 'genocide' only applies to killing humans, but you get the idea, I'm sure)