A.T.
I think that the ratio issue is definitely a valid concern. However, I think that you may be a bit overprotective! (sorry!) But,could his stranger anxiety have something to do with the fact that he isn't exposed to much?
There really is no way that they could sanitize all the toys after each service, and honestly - germs are everywhere! You can't protect your child from everything because when he finally DOES go out into the world he will get sick all the time and be in culture shock!
I would consider enrolling him in a preschool part time to try to help him with his anxiety so that when he starts school he will be able to learn and not have to spend the first year learning that he DOES have to deal with other people in life!
I am not saying this to be mean, I promise. I am saying it because I am a teacher and I SEE the results of so many children who are babied and overprotected. They are WAY behind their peers emotionally and it takes me at least 1/2 the year to get them to understand that school is NOT home - they DO have to follow rules.
I know it is really hard to leave him, but for his own good do so (maybe somewhere besides the nursery at your church though, b/c they do sound too full for one person). And as for the snacks - he can go an hour or so without drinks and snacks! He will be fine!
Don't let YOUR anxieties take over what is best for him! I say this out of kindness, not anything else!