I think they should absolutely allow him admission. D1 schools lower their academic standards all the time for the sake of allowing admission to good athletes - if they are wiling to do that, they should be willing to accommodate an autistic student.
If what his parents say is true, that running has given him unprecedented focus to learn and succeed in school, then he should absolutely be given this chance. As "NOP skeptic" said, he needs only to keep a 1.8 to stay in school. He is apparently able to keep an 84 high school average, so with the appropriate accommodations I think he could keep a C average in college.
I don't think a kid should be denied a chance to run at the college level, especially when so many athletes fail courses and barely scrape by in school despite their higher intellectual capabilities.
He can't even hit the minimal standards required for those lower standards for athletes. Also if he has an 84 either he is not actually taking classes, or he scored like a 400 on the SAT because the sliding scale makes it pretty easy to pass if you have a decent GPA.