Edit: if you were being sarcastic, sorry, I'll go get an energy drink!
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.
Ugh. Citing that does not signal you as knowledgeable about computers, it signals you as profoundly ignorant. In the real world, viruses for Windows can and have been served by Unix systems running entirely different architectures via exploited websites. We don't even have to get into the theory of the matter, we can demonstrate cross-OS virus transmission in practice. Bits are, quite profoundly, merely bits. They do not have a Mac or Windows or Alien color: http://ansuz.sooke.bc.ca/entry/23
While I'm sure beyond a shadow of a doubt this was accidental, the idea that a fundamentally telepathic and possibly hive-mindish species of alien may have advanced computers and no concept of computer security because they have no concept or biological possibility of generating a computer hacker is actually a respectable sci-fi speculative idea.
Keeping around one particular instantiation of a DNA sequence because it might be useful against a low-probability event isn't useful, because in the grand space of potential DNA-based solutions to such a problem, the smallpox virus is vanishingly small and effectively no different from just deciding to hook a random number generator up to a DNA sequencer, shoving the results into a virus shell, and hoping for the best.
Unless they have cellular machinery that can reproduce smallpox, there is zero chance of such an attack being successful.
And the odds of an alien species having biochemistry compatible with earthlings is vanishingly small.
Besides that, our chances against a civilization capable of interstellar travel are a rounding error above zero. I would say zero, but they may be so alien as to mistake us for the rocks we live on.
For all we know, "they" engineered smallpox and are actually immune to it. It was sent to Earth as an engineered precursor to their arrival.