The three cops who were acquitted were originally indicted. An indictment is a far lower legal standard that "beyond a reasonable doubt". A critical part of the MD AG's case was a corroborating witness i.e., one of the police officers. Again the case wasn't prosecutable under civil rights violation and conspiracy. Aggravated assault was probably the strongest charge and that was against the police officer who drove the van. Maybe the arresting officers for excessive force. However, we're not privy to all the evidence. 

The MD AG clearly stumbled when she believed that two arresting officers who were white "made the case". Gray "rabbited" when the two officers were conducting an area drug sweep. Running from the cops isn't evidence of guilt but for a frequent flyer like Gray, wearing a backpack, in high drug trafficking area? The MD AG believed the two white arresting officers formed the basis of the conspiracy to violate Mr. Gray's Civil Rights.