I don't see small pox as being unique. If we get rid of it, we need to get rid of everything else. I think we still keep ebola, for example. Frankly, there is simply no way of knowing the future (though I agree, there's no way of ensuring security of samples into the future, either). We worry about destruction of rainforests, because we have no idea what cures and solutions we might find in the undiscovered life within that could be lost forever. Likewise, we simply don't know what today's "horror of horrors" could find beneficial use, some day.

In the event that we are invaded by aliens, I would count the success of unleashing small pox on them as being much greater than Jeff Goldblum infecting them with a virus from his macbook. :P

When it comes down to it, though, I don't think there's a right answer. We just have to make an educated judgement call. Maybe the kind of judgement call where we respond to things like "but if we torture people, we can find terrorists!" with "but that's not the kind of people we are". Maybe we really do need to be the kind of people who say we're not willing to risk exposing innocent people to this for some future that we are only guessing about. Or maybe it's enough to simply map the genome and keep the data on it archived, while dumping the actual real deal.