Austrian psychologist Asperger published the first definition of Asperger syndrome in 1944. In four boys, he identified a pattern of behavior and abilities that he called "autistic psychopathy", meaning autism (self) and psychopathy (personality disease). The pattern included "a lack of empathy, little ability to form friendships, one-sided conversation, intense absorption in a special interest, and clumsy movements." Asperger called children with AS "little professors" because of their ability to talk about their favorite subject in great detail.
Asperger was convinced that many of the children he identified as having autistic symptoms would use their special talents in adulthood. He followed one child, Fritz V., into adulthood. Fritz V. became a professor of astronomy and solved an error in Newton’s work he originally noticed as a child. Hans Asperger’s positive outlook contrasts strikingly with Leo Kanner's description of autism, of which Asperger's is often considered to be a high-functioning form. In his 1944 paper, Asperger wrote:
We are convinced, then, that autistic people have their place in the organism of the social community. They fulfil their role well, perhaps better than anyone else could, and we are talking of people who as children had the greatest difficulties and caused untold worries to their care-givers.
Near the end of World War II, Asperger opened a school for children with autistic psychopathy, with Sister Victorine. The school was bombed towards the end of the war, Sister Victorine was killed, the school was destroyed and much of Hans Asperger's early work was lost. It was this event that arguably delayed the understanding of autism spectrum conditions in the west.
Based on this information (fetched from Wikipedia), I think it would be safe to assume that Aspies would have been treated like normal Germans and certainly not be put up for extermination/euthanasia.