Short answer is it depends.
Because the victims were only knocked unconscious, they would still have been breathing in the fire and would presumably have died as a result of smoke inhalation. If they died from their head wounds before the fire, the obvious sign would have been a lack of smoke in their lungs.
That leaves an external and internal examination of their head. Externally, you would be looking for a contusion and/or bruising. Internally, you'd be looking for a skull fracture and/or a contusion on the brain, with some bleeding possible. The question then becomes the survivability of the body in a structure fire.
Bodies in structure fires can vary widely in condition. Depending upon how the building collapses, bodies can vary from virtually no damage to extensive damage with massive amounts of skin being burned off. Assuming a lot of destruction to the body, the only sign remaining would be the skull fracture, if that had happened. Minor damage to the body would leave the other signs.
However, these injuries would also be consistent with something falling on them during the fire. This could complicate the situation during a criminal trial for the slugger.
If the ME was responding to a suggestion in this type of situation, I'd question the competency of the ME. This stuff should be gross enough to be seen during the autopsy. An ME that is responding to suggestions is going to have a problem testifying that the cause of death was whatever beyond a medical certainty.
I was a volunteer firefighter/EMT and am still impressed with how much and how little can survive a structure fire.
Best of luck,
Jim Clark-Dawe