Juana had a chance to throw the pearl away, but she decided against doing it. Why was it so?

She decided against it because she realized they weren't safe and needed to go away.

While walking on the beach, men accost Kino in search of the pearl, which is knocked from his hand and lands on the pathway. Juana soon sees Kino limping toward her with a stranger whose throat has been slit. She finds the pearl for Kino, and tells him that they must go away before daylight.