Juan Tomas says Kino "You have defied not the pearl buyers, but the whole structure, the whole way of life. I am afraid for you". What does he mean?

Kino has upset the natural social order of things by refusing to sell his pearl. This puts everybody's business in jeopardy. Now the pearl buyers are angry with Kino and many of his friends and neighbours. Kino's people know they are being cheated out of money: that is just the way of things. Kino's refusal to be cheated changes the natural balance of things.