If we're going to discuss comets or asteroids carrying a disease that would affect humans, lets ponder the odds. I'm not an expert on the subject, so please point out to me if I'm off base here.
First off, the critter has to be able to survive in space. Space isn't a particularly hospitable place, being a vacuum featuring temperature extremes, cosmic rays, and lack of oxygen. Then, it actually has to hit earth and survive re-entry. Assuming the critter survives that, it has a 70% chance of landing in the ocean, which greatly reduces its chances of infecting a human. Even if it hits land, it has a better chance of landing somewhere pretty much empty than it does landing somewhere populated.
Next, it has to be able to survive on our planet, which is a rather different environment than outer space. It also has to compete with the billions of other lifeforms which are adapted to live in our environment. Considering the mass of the asteroid compared to our planet, it is much more likely that one of our bugs would wipe the space one out simply because there are more chances for it to occur, just like wolves in adventure mode.
So lets say the asteroid lands in the middle of new york city. It thrives in our environment, and has ready access to humans. Lets even make the leap that it has "infected" a few and is highly contagious, and immune to any of our medicines and our immune systems. It's a rather big leap, but lets make it anyway. The trouble is, the vast majority of bacteria and viruses are harmless to humans, so even if there was an "epidemic" it would most likely just be a scientific curiosity rather than a catastrophe.
Unless I'm missing something big, I think it's more likely that a future version of dwarf fortress will end man as we know it than some alien super bug.