But before the end of the service, a usher Tristan and his family asked to leave the reason he was disrupting fellow parishioners, Rimmer said.
In a bitter letter addressed to the college dean, Rev. Dr. Stephen Cherry, Rimmer's complaints as a false excuse to "lessen the satisfaction" of tourists visiting the chapel and who found his son's form of worship offensive.
"My son may not be able to speak, but he knows very well what is going on around him," he wrote. "He's not even ten years old and he knows he's unwelcome."
Rimmer, who teaches astrophysics at the University of Cambridge, said the incident was not the first time his family had been asked to leave a church, but marked the only occasion a member of the priest asked to remove them.
"Can I suggest you put a sign on the front of the chapel where you clearly identify which categories of people are welcome and which are not?" he wrote.
"Yet as dean I take responsibility for the chapel's whole life, and in that connection I express my unreserved apology and intention that we will do better in the future."
In an update, Rimmer said he was "touched" by the many dozen churches who invited his son to attend and worship the way he wanted, as well as the countless parents of children with autism who offered their support.
The dean met with Rimmer, who said they had a positive conversation about how to make the chapel accessible to all their parishioners.
Rimmer and Cherry did not immediately respond to requests for comments.