Realistic penalty required
I think two issues are going on here, firstly whose computer system it was and the hacker's background.
1) As it was the Pentagon's computer system, there will be a huge amount of lost face. The fact that someone managed to hack in to the system suggests that security was lacking. There are bound to be many red faces. The attack on esteem would be viewed more seriously than any damage (if any) that was caused.
2) Asperger's syndrome is an autism spectrum disorder, some of the characteristics of the disorder include a poor ability to read other people's motives, body language among others, he will be at risk in a prison environment. What is required is a penalty that is suitable.
A major problem with Asperger's syndrome is that in the majority of cases, there is little outward sign save for somewhat eccentric behaviour (in some people) to suggest that there is anything wrong.
I wager that if McKinnon had a disability that was visible, there would be no chance of him being shipped off to the states. If the American's get their way, it would be imperative that he has suitable backup support and have access to professionals who have an adequate knowledge of autism spectrum disorders to argue his case.