Yes--Burke could have caused the blunt force trauma to JonBenet. But, since her cause of death was asphixiation combined with blunt force trauma, I can't rectify in my mind how Burke would have strangled her in the fashion that she was. And if the strangulation marks on her neck had occured postmortem, as a way for the parents to 'cover up' for the Burke-caused blunt force trauma, the coroner would have been able to determine that during the autopsy.
I believe there is other, indirect, evidence that Burke was not involved, but the above is my strongest reason.