Found this in the Gawker comments on a post related to the Grand Jury indictment:
Seems plausible to me.
I am in law enforcement and at one training, Interview Tactics, the presenter was a former detective who followed this. His theory was that Jon Ramsey sexually abused the son as a child, but when JonBenet was born and came of his preferred age, he began abusing her instead. His theory was that the boy, angered by the lack of attention and "love" from his father and the fact that the "love" was now being given to JonBenet, killed his sister in her sleep. The parents found her, and knowing what could happen if the truth came out (son arrested and charged with his sister's murder as well as Jon's sexual abuse of both children, leading to his arrest and charge with criminal sexual abuse of a child victim) that it would destroy everything, so they chose to cover it up, in turn, leaving their daughter dead without justice, but their son safe and the husband getting away with his crimes. Obviously a lot of this is theory, but we spent hours going over interviews, the ransom note, as well as the behaviors of the Ramsey's and it all seems to fit.
Seems plausible to me.