Hopefully, you will get some advice from other parents of older children with autism who can give some advice, but here's my take on it.
I'd just tell the CM at the scan point that he has special needs and won't be able to do the scan. My best guess is that they won't make him try unless he wants to, as long as you explain it (after all, they don't want him upset any more than you do).
If he's using a special needs stroller or a wheelchair, they probably won't even ask. My youngest DD has been an adult (at least at WDW) for a long time. They see the wheelchair and don't expect a scan. My DH takes her thru - he tells the CM he is putting her ticket thru and the CM triggers the machine to take it without a finger scan. Then DH puts his ticket in, scans his fingers and pushes DD's wheelchair thru the gate.
You could also try going to the Guest Service location outside the turnstiles and explain your situtation. They may be able to help you with some advice and/or a card or something that explains he can't do the scan. I'm sure you are not the first people to run into this situation, so don't worry.
I don't know what your child's level of being able to cooperate is, but you may find that he is able and willing to do it if you can watch some people using the scanners and talk about what it feels like/sounds like, etc. before he tries.