Apparently he was planning to leave the the gang and so Chino killed him and dumped his body near the rocks. While at the scene, Rafael's mother, Eva, tells Dexter Morgan to "hunt Chino down and murder him like a dog."
Before getting the chance to testify against Chino, Eva was killed. Even if she did get the opportunity however, she would have little credibility, being a drug addict. At the crime scene, her young daughter (Rafael's younger sister), is carried away by a cop, much like Dexter Morgan was carried away by Harry Morgan from the Shipping Yard, after his mother was butchered in front of him and his brother Brian Moser. It is because of this that Chino becomes a top priority.
When he is about to kill Chino, Dexter has a picture of Eva's daughter on the walls. Chino states that he never killed a child, but Dexter responds: "You killed most of her," referring to her lost innocence at the deaths of her family members.