One other point, much of what I've read concerning the science of the assault on the child is that the hit to the head happened AFTER the child had started to be choked by the garrote. Was Burke mature enough to even think of using a garrote on his young sister just for fun?
The knots found on the garrote were sophisticated... Not the type of knots a young kid would do.
There's also evidence that Jon Benet fought against the person trying to garrote her.
So... Burke hits his sister with flashlight, nearly killing her.
His mother comes across what is going on, and starts to garrote Jon Benet to make it look like an intruder did it, but Jon Benet starts to come too, starts to fight the use of the garrote and her mother figures, "Well she's close to death, we don't want to see Burke held responsible for this so I finish her off with this garrote."
No, I'm not buying it.
Now that's not to say I'm 100% convinced that someone in the immediate family didn't do it, I'm just leaning much more in the direction of an outside intruder.