Some of the worst reactions to my son's behavior have been in church. Lots of disapproving looks etc. All that said two weeks ago my son made his Confirmation in the Catholic Church which is a major accomplishment.
It was a long road to go through 8 years of religious education. The nun who was the director of the program had a really hard time accepting my son. I always felt like she was worried his behavior somehow reflected badly on her. I even asked her "what are you afraid of Sister?"
I could go on and on but my advice is if you enjoy going to church then go. Bring distractions for your child. In the younger years we had books, snacks, drinks and whatever else it took to get through Mass. Many times I wanted to give up but it was important to me so we kept going.
MY son started to cry very bad at the time they started the songs because it was very loud for him. I had to take him outside but he continued crying. I had to leave from the church.
I'm glad you called her out on her attitude. When we attended the parents meeting for first communion, the priest told the group that if a person doesn't receive communion there is no way he can enter heaven, I wanted to punch him in the head. I thought that he was the most ridiculous priest I had ever met. I got help from people in this group, I called my diocese, I researched. There are a ton of resources for Catholics with autism. That religious education director should look them up.
I got our church to starts a special needs ministry... So far so good!
Poor little guy. You know what's right for you son. Whatever he needs, give it to him.