Burke Did It
JonBenet can't sleep so she wakes Burke and the two of them have some pineapple together. One thing leads to another and either 1. Burke gets upset and swats her with the Maglite or a baseball bat or 2. Burke attacks her sexually, she resists and he swats her. In either case, the parents are awakened by the commotion, see what's happened, and are afraid to call 911 because 1. Burke is now Patsy's only remaining child and she's afraid he'll be arrested; 2. John is alarmed by the injuries to JonBenet's vagina and is afraid he'll be blamed for molesting her, because no one could possibly believe nine year old Burke could be responsible.
From here on out, we have a scenario almost identical to Partners in Crime (see previous post), including all the many fantastic elements in that one. (We can add the option that Burke could be responsible for the "garotte," making it with his knife and using a knot learned in cub scouts. Hard to say why he'd do that, but hey boys will be boys.) Only in this case we also have the fantastic idea that nine year old Burke was sexually active, and also that he would have been strong enough to deliver a blow that, according to experts, could have felled a grown man. Of course, it's possible that the sexual attack and garotte were both part of the staging, but once again we can't help but wonder why a head wound would not have been reported as an accident.
Kolar goes into much detail regarding the possibility that Burke could have been sexually active and having an incestuous relationship with his sister, but he says little about why two otherwise normal parents would suddenly morph into characters from a gothic drama to protect a child who 1. just murdered their beloved daughter and 2. was too young to be prosecuted in any case. There's really no more to be said about Burke Did It, because oddly this possibility sheds no real light on the case at all, only making things even more fantastic than they already appear to be.
So here too we are in the Twilight Zone, I'm afraid, with Burke playing the role of little Chucky, the ventriloquist's dummy.
It's possible, of course, that Burke could have been sexually molesting JonBenet and that John would have wanted to cover it up out of fear that he'd be accused. Patsy could easily be eliminated from this scenario, which would make it very close to the one I've proposed, in which John is the sole villain. I find this possibility more fantastic than any of the others, but as there is no way to prove Burke could not have done such things, we cannot completely exclude it. The problem for Kolar is that this sort of Burke-did-it scenario eliminates none of the contradictions of the case as he sees it, and only adds more elements that seem highly improbable.