Both Patsy and John received the same GJ idictments - they couldn't both have known the person being assisted had committed the crime of murder unless you believe they both murdered JonBenet - and in that case they would have both been charged with murder. So no, the indictments make it perfectly clear who the GJ thought was the murderer, who covered it up, and who didn't protect JonBenet from a dangerous person.
I can think of a scenario where the GJ had enough evidence to show that Patsy and John jointly covered up the murder, with the GJ not knowing which one had actually committed it.
So for example -
JonBenet had been sexually assaulted priorly, and both parents knew this or one knew and was forced to tell the other because of what happened.
That night JonBenet suffered a head trauma (she fell, she was pushed, she was hit by Patsy, John or Burke) with or without a possible neck abrasion.
John and Patsy assessed the situation and thought she was dead or dying or too severely brain damaged to live without long term life support. If she was taken to ER she would be examined as a possible victim of a physical assault, and the
prior sexual assault/abuse may come to light.
John and Patsy together decided to make this look like a strangulation by an intruder, hoping that the head wound may be missed. It wasn't bleeding, there was no visible lump or swelling, and they arranged her hair in a ponytail to sweep over the top of the wound area.
One of them also thought of staging a sexual assault because they thought it might cover prior sexual violation. The other one didn't agree with that aspect of the staging because if they were ever linked to the murder, what if one of them broke down and confessed or a child said something that gave the game away, they would also be linked to knowledge of and/or participation in prior sexual assault, so they cleaned up and tried to remove evidence of that.
The GJ don't know who did which aspect, but they know that both of them do know at least, even if they didn't do it. Patsy knew because she wrote the ransom novel, John knew because they don't believe he read that ransom novel and was taken in by it, and they believe he knew where the body was, and then tried to get the hell out on the first plane he could arrange and lawyered up.
So in this scenario, the GJ knew both parents were involved in the cover up but they didn't know which one did the killing act. Maybe the GJ couldn't be certain whether JonBenet died exactly as a result of the head blow or the strangulation, or which came first, or if JonBenet might have survived on life support after the head blow then whoever did the strangulation killed her.
There isn't enough evidence to say who killed (murder indictment) but there is enough evidence to show both knew who committed which aspect, and acted afterwards to destroy evidence and hamper the investigation.
I don't know, there are probably holes in my theory, but I don't think it can be said that the only interpretation of the indictment is that Burke is the only possibility. The lawyer on CBS didn't say it was 100% clear, she said both parents could be indicted with assisting each other but it was her opinion that it related to a third person.