Suppose a disease wiped all NT's off of the face of the Earth within the next 2 months. Supposing only those with autistic genes would have immunity, I don't think much would change at first. We would probably all continue to do our own thing, until we would discover that it wouldn't work. We would have to come together and establish a new economic system (hey, who is going to work at WhackDonalds?). Whether or not that would actually happen, I have no idea.
But, suppose it was the other way around. If all aspies and auties were to be removed from the population, I don't think it would be that significant. All I can think of that would happen is that technology would advance at a much slower pace, or even go down quite a bit when the few people who understand it are dead. Still, I don't think it would have that much of an impact as there are still smart NTs in the world.
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Remember, all atrocities begin in a sensible place.