Did Mr.Hooper know that he has upset the members of his church?

No, he doesn't. Mr Hooper goes on with business as usual.

"After a brief interval, forth came good Mr. Hooper also, in the rear of his flock. Turning his veiled face from one group to another, he paid due reverence to the hoary heads, saluted the middle aged with kind dignity as their friend and spiritual guide, greeted the young with mingled authority and love, and laid his hands on the little children's heads to bless them. Such was always his custom on the Sabbath day."