I think the jury excluded the possibility of Rudy carrying a rock up the wall because he needed his hands to hold onto something (not sure what) while attaching himself to the flat, vertical wall. He couldn't have climbed the wall with the 9 pound rock in hand. To suggest he put the rock in a backpack, and smashed that pack into the window would also require some interesting manoeuvring ... risky in the sense that he would need both hands and feet to cling to the wall. Even if he did use the pack to break the window, glass would fall to the ground below. This seems obvious because in smashing the glass with the pack, some glass would attach to the pack and the pack would be put back on his shoulder ... thus giving a high probability that some glass would fall to the ground. Furthermore, gravity would cause glass to fall on the outer window ledge. In order to hoist himself in through the window, at least some glass would fall onto the ground below.
It seems that most people agree that some glass should have fallen on the ground below, so the explanation for the absence of glass is to accuse police of not properly investigating the ground below the window. According to the jury, the ground below the window was investigated, and there was no evidence of broken glass (they did find a dinner knife that was not connected to the murder), or of anyone having stood on the damp ground. Furthermore, since the ground was damp, anyone that walked along that narrow path beside the house would have had some dirt, leaves, or grass on their shoes. There was no evidence in Filomina's bedroom of any debris from the ground outside the window.
There were many reasons for ruling the break in staged, and that presented a very serious problem for Amanda and Raffaele.