Leprosy is one of my special interests.
Foucault argued in "Madness and Civilization" that madness - a concept vague enough in this conception to include what would today be called Autism Spectrum Disorders - was basically created to fill the social void left in the wake of leprosy's decline in Europe. So the comparison has some support - not in terms of "autism is as bad as leprosy" but "hey are we maybe treating autistics the way we used to treat lepers?".
Bear in mind also that leprosy was long considered a divine disease. Supposedly the afflicted would not need to wait in purgatory but would ascend to Heaven upon their deaths, because through their leprosy they had pre-paid their penance in this life, earning them a Fast Pass to the afterlife.
So, when speaking at the Vatican, comparing autism to leprosy comes across, to me, not so much as "Eww look at the autistics, they're gross like lepers" and more like "Autism. like leprosy, might better be thought of as a great blessing that comes with a great burden, rather than a curse or affliction."
On the other hand - Jesus healed the sick and the lame, but he cleansed the lepers.
I have no idea what Ms. Wright's motivations for making this comparison were.
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From start to finish I've made you feel this
Uncomfort in turn with the world you've learned
To love through this hate to live with its weight
A burden discerned in the blood you taste