I read the article and skimmed the 83 comments to date. It was an early release for the Sunday paper.
It's interesting that the author was representing both sides, pointing out the accommodations made, the successes of the program, and downsides.
Even the descriptions of the positive side of the program seemed to have negatives in them, for instance noting the employee who talked about train disruptions every time there was a storm (which I gather happens regularly in Copenhagen), and the employee who didn’t bring in a cake on Fridays.
The story made clear that this program has so far had a 1 in 6 success rate at planting employees with employers, and the difficulty in explaining the failed placements to hopeful parents.
I'm not sure if some of the story is the result of cultural differences, where something’s are more easily discussed in Denmark, but they would never be conveyed in a business/cultural story in the New York Times. I believe that the cultural aspect of the story may have played a part in the article.
My conclusion after a first read is that the story was a fairly realistic portrayal of the subject. The comments were the usual split of comments on a story about autism. I expect many more comments after the story has circulated on the web for a few days.
Edit: Spell Check