I agree that other scenarios are less likely than the interrupted burglary-gone-wrong Charlie has described a number of times. However, I continue to hold to a theory that allows for a "kinder, gentler" Rudy, regardless of how unlikely it is.
I still don't see enough evidence showing Rudy was in Filomena's room. I also don't see why, if he were in the middle of a burglary, he would feel like he had to take out Meredith for catching him. He could just jump out the window or wait until she went to her room and closed the door. He had little to fear from getting caught -- he had gotten away with several burglaries already. The exception might be if she walked in when he was sitting at the kitchen table drinking orange juice and she justifiably freaked out.
I don't see any reason why Rudy and Meredith couldn't have just crossed paths as Meredith came home. Maybe Rudy was near the cottage or maybe he was out wandering around. He asked Meredith if he could use the bathroom and she said okay. She did know him. I think it is more likely that he drank orange juice before going to the bathroom, but that would have to mean that Meredith offered him some juice, which doesn't seem that likely. He could have poured the juice for himself after using the bathroom.
I agree, partly (I also don't fully agree with aspects of Charlie's scenario). I think Rudy's first impulse on realizing someone had come home would be to try to escape, not to sneak up to Meredith's door, run in and attack her. So it seems more likely to me that she encountered him as he was trying to leave and somehow things escalated from there. Perhaps she heard him trying to open the door and came out of her room to see what was going on.
One random scenario I've considered would explain the mysterious lamp: perhaps Meredith had gone to her room and had partly undressed for bed, when for whatever reason (and thinking she was alone in the house) she went next door to borrow Amanda's lamp. Coming out of the room she encountered Rudy looking for a way out of the cottage, screamed and ran back to her room, dropping the lamp near the door as she tried to close it. Rudy ran after her to try to keep her quiet, probably with some idea of explaining his presence there, and again things escalated from that point.
But I do agree that it's also possible they crossed paths as Meredith came home, and really not all that unlikely she might have allowed him in, knowing he was a friend of Giacomo's. As Grinder says, there does seem to be an element of needing to see Meredith as the 'good girl' in all this (inevitably making Amanda the 'bad girl' who let him in), as if letting him in would say something negative about her. In reality of course, it's the kind of gesture that happens everyday, almost always without anything bad happening.
This adds a significant twist to the possibilities for what happened. If Rudy saw Meredith in the process of undressing, that might have given him ideas. This is not helpful to my theory, though, as I doubt Meredith would start to undress if she knew Rudy was in the house.
Anyway, my "kinder, gentler" Rudy theory is that after his unsuccessful attempt at seducing her ended in a brutal attack, he took her phones and locked her door because she was still alive when he left; he assumed she was not mortally wounded and she would try to seek help, and he wanted to delay that. Due to a sudden twinge of regret, he threw the rock through the window as he left, hoping the noise would alert someone to the possibility of trouble. That's the same reason he left the phones in a place where people would find them easily, rather than disposing of them more effectively.
Yes, if Meredith was partly undressed when they ran into one another it would help explain why the assault turned sexual. Not that it can't be quite easily explained even without that, obviously. But as you say, that's only a possibility if Meredith didn't know Rudy was there.
The only flaw I can see in your broken window theory is that the shutters were found pulled together, and why would Rudy have bothered doing that from outside the house? Especially if his intention was to alert people to possible trouble.
ETA: Don't you think the towels show remorse?
I agree with you there. The alternative theory - that he carefully placed towels so he didn't get blood on himself during a post-mortem sexual assault - has always seemed unlikely to me, an attempt to simplify the crime by turning Rudy into an absolutely calculating, cold-blooded psychopath (who nonetheless stopped short of an actual rape). Since he presumably didn't enter the house intending to kill anyone, conflicting and panicked emotions afterwards seem more probable. I guess my theory falls somewhere between your 'kinder, gentler' Rudy and the 'cold-blooded psychopath' theory of Rudy which predominates...