I think Burke did it and then the parents tried to think quick and cover it up.
John Ramsey broke the window previously as he told police, but he never quite got around to getting it fixed. It had been playing on his mind recently, and lying awake at night sometimes his mind wandered to scenarios such as an intruder breaking in and even worse kidnapping his celebrity daughter JonBenet. He thought about how he had read there were so many sex predators in the area that might do things, and how it would be all his fault if they did. By morning such wild scenarios seemed extremely unlikely, but he still had to get around to having that window fixed. So that scenario probably already occurred to him.
Burke was eating the pineapple and Jonbenet stole a piece. Maybe she knocked over the bowl and all the pieces fell on the ground.... this could make him extremely angry and lash out violently. So he hit her with a hard object, he thought it would be like the golf club before (after which she was fine).
When Burke hit Jonbenet, she collapsed and Burke's demeanour quickly changed and he cried out for mommy. Patsy found Jonbenet, knew she was dead and wailed and mourned. Patsy had images of the headlines the next day on what happened to the beauty queen pageant Christmas day, butchered like Jamie Bulgar, by her own brother, and how Burke would be taken away forever. John woke up or maybe Patsy called him and his first half-asleep instinct was an intruder. Then when he realized what had happened, like Patsy he was extremely afraid of losing both his children. So the first thing that came to his mind was let's pretend an intruder did it.
It may seem a bit strange to accuse mature professional adults of being influenced by movies, but it can happen to us all. Instead of doing the straightforward thing of owning the mistake but fully protecting their son, or even staging some sort of accident, they went the totally dramatic route. Watching so many movies he had a warped perception of how rare/likely this scenario is. Whoever wrote the ransom note was certainly heavily influenced by movies as from the quotes in it, and there were a lot of movie posters around the house. Sometimes people come up with things late at night that seem totally daft the next morning. But once they had done this, they felt compelled to stick with it.
I can only think that the reason they gave that specific amount of amount in the ransom note was that John was trying to make it seem like the "foreign faction" had private information that only he should have had access to, so trying to put on they were this sophisticated group that had infiltrated many levels and had a lot of resources. But this would run counter to the "neighbourhood " theory, which is the only serious competing theory.
A lot of people crack under police pressure (which is to their credit, only a complete psychopath can live out a lie forever). The Ramseys felt morally vindicated because most of what they were saying was correct "I did not kill my child", and then they only had to remember a couple of things about finding the ransom note and the easiest thing was that Burke was asleep the whole time. They told Burke to say that he was asleep the whole time.
But even if we're 99%+ sure, it's still not 100%. The justice system shouldn't convict on 99% certainty. I would have to say though the most ridiculous thing of all that happened was the "letter of apology" to the Ramseys that "exonerated" them based on the DNA. That was quite the kick in the teeth to the remains of Jonbenet Ramsey.
