Why do you think the Baptist minister was all silence after his interview with Miss Emily?

Of course, we are not actually told why.  But we can guess from the context.

In this part of the story, Emily has been going around town with Homer Barron.  The people of the town think what they are doing is improper and they send the minister to talk to her.

Given that context, it seems clear that she has in some way told him to mind his own business.  I don't know if she told him something scandalous about her relationship with Homer or if she was just really rude to him.  I think it is one of those two things.