Though his remains were partial, it is entirely possible to tell breaks that occurred at time of death from those that occurred postmortem. If enough of him was found, they may have been able to see those breaks. If the object she used had a particular shape, for example, was square or had a defined edge, it may have left tool marks in the bone.
An example for illustration. A hammer leaves very identifiable marks in a skull, whether the head is used, the claw end, or the side. There may not be such clear marks in Quinton's bones, but there may be tool marks that show he was beaten with an object (that the damage wasn't caused by, say, a fall), and that that object more than likely inflicted injury sufficient to cause death. Those marks would be different from the postmortem damage, because they occurred while Quinton's body was alive, while he could still bleed and bruise, and while his bones were still supple and flexible.
Tl;dr, it is possible to see tool marks on bones, and tell that those marks were left when the person was alive, rather than sometime after death, ie. in the garbage truck or at the landfill. It's very difficult to do, but this is what forensic anthropologists train for. They're the folks whose whole bag is bones. They leave the soft tissues to the pathologists.
Also, if he was bludgeoned to death, it may be why they were so sure he was dead so early. They may have found castoff patterns in the house, visible with the naked eye or with luminol, composed of blood and/or brain tissue. I speculated early on that they'd found some kind of biological evidence not compatible with life, a large amount of blood, or something like brain tissue, and I still think I have a good chance of being correct.
MOO