The pearl is a symbol of innocence corrupted.
One of the motifs of the book is the songs. Kino hears the music of the pearl as he walks along. The pearl started as a symbol of possibility, and a chance for a brighter future.
The music of the pearl was triumphant in Kino's head, and the quiet melody of the family underlay it, and they wove themselves into the soft padding of sandalled feet in the dust. (Ch. 6)
As time goes on, Kino is unable to turn the pearl into the future for his family that he needs. Coyotito, in danger from the poison of the scorpion bite, is now in another kind of danger when he is shot.
Kino is so angry when the dream turns on him that he decides to throw the pearl back into the sea. He realizes that it was bad luck. It never manifested its purpose. Instead, it brought only misfortune.
And in the surface of the pearl he saw Coyotito lying in the little cave with the top of his head shot away. And the pearl was ugly; it was gray, like a malignant growth. And Kino heard the music of the pearl, distorted and insane. (Ch. 6)
He feels like he has lost everything because he got drawn in to the Song of Evil. The pearl did not represent the Song of the Family like he thought. He was manipulated by pride and greed into believing that he needed more. It ended up being the doom of his family.
Kino was not a greedy man, exactly. At the beginning of the story, he is a simple man enjoying a simple life. This is not the story of a man corrupted by greed or ambition. It is the story of a man who wanted to give his family everything, but lost the thing he loved the most in the effort. The pearl was just too much temptation to bear.