"So many people" in Meredith's six weeks of being in Perugia? And not only that, you can pretty much eliminate every female Knox knew, so Meredith's circle of Perugia acquaintances is more than halved at a stroke (assuming she had more female acquaintances than male). Next, it was a public holiday with religious/family associations, so many students were away from Perugia at their families' homes that night. So in fact there were probably only a very small number of males who were known to Meredith, who were in Perugia that night and who didn'r have a good alibi. Guede would have quickly and easily been able to reason this out.
But I agree with you that this is purely a hypothetical discussion, because Guede threw the rock from the outside before the confrontation/murder. However, I disagree with your opinion that Meredith came back before Guede had the chance to enter through the window. There are two main reasons for my disagreement: firstly, if Meredith arrived home at that point, she would almost certainly have seen the broken window (the exterior shutters would, by definition, almost certainly have been open at that point, exposing the broken pane). I think that she would have wanted to make phone calls immediately (to the other girls and/or the police), and might not even have been happy entering the cottage - even if Guede offered to be her "protector". And secondly, the broken window shows clear signs of someone removing addition glass up the side of the frame in order to be able to access the catch.
Therefore I think that Guede did indeed scale the wall again, remove this glass, unlatch the window and enter Filomena's room. I think that once he was inside the room he almost certainly pulled the exterior shutters back inwards, in order to conceal the broken window from anyone outside the cottage. That's also why it makes sense that Meredith didn't think anything was amiss when she returned home at 9pm: all she would have seen as she approached the cottage would have been Filomena's exterior shutters.
And that actually leads me to something else that I haven't thought of before now. If Guede indeed entered via Filomena's window, then went to the fridge to get a drink before going to the bathroom to defecate, then it's entirely likely that he might have left Filomena's door open (he wasn't expecting to be interrupted inside the cottage after all - all he would have been concerned with was concealing his presence from anyone outside the cottage). So it's entirely possible that Meredith came home while Guede was on the toilet, grabbed a mushroom from the fridge, and headed towards her room. But at this point, Meredith would have had to pass right by Filomena's bedroom door; it's entirely possible that Meredith would have glanced into Filomena's room (if the door was left open by Guede), and noticed the broken glass. She might then have either made some sort of exclamation of shock and fear, or she might have called out for anyone who was there to get out. At that point, Guede would have had little option but to jump off the toilet without flushing and confront Meredith - who would have been essentially standing between him and his escape route.
In addition, if this is what actually happened, it fits in slightly better with Guede's movements after the murder. If he never tried the front door before the murder, he probably wouldn't have known that a key was needed to open it from the inside. Therefore the bloody shoeprints leading towards the front door might have been from Guede's first attempt to leave the cottage. As soon as he reached the door and tried to open it, he'd have found out that a key was needed. This therefore necessitated another return to Meredith's room, in order to search through her bag for her keys. After locating the keys, Guede left Meredith's room for the last time, this time with no blood on the sole of his shoe. He paused to lock Meredith's door with the new-found keys (in order to delay discovery and give him more time to try to establish an alibi), and exited via the front door.
Just a thought......
