yes autism is covered under ADA.
I really think this is a case of the crew being really insensitive and it came to bite them back and it end up in the news, and the airlines are gonna have to do a bit of CYA and payouts to quiet this down as the ADA groups tend to not let things slide under the radar.
I hope the pilot is aware that he could be held accountable for slander and the FA could be charged with child endangerment and assault for making a comment like that.