Of course if a person has been stabbed in the throat, to try and stop the blood with towels would be of little use (although there was a time I cut my arm and it was bleeding profusely, and I did use a towel to staunch the flow before going to the ER). I assumed Guede (or the others) were too stoned to realize the futility: the stabbing could not be reversed.
But what do you think they were used for? As they were blood soaked (are there picture of them anywhere, btw?) I would assume they had been placed on her neck.
ETA: Or were they used in the clean up? Did they wipe the bathroom floor? But then, if Guede knew this, the lone wolf scenario is thereby bolstered. I had assumed Knox would have used them in the clean up. But I assumed Guede had already fled. So again, did he have access to this info in the news?
I don't think the towels were used to help her at all. I think Guede placed the towels around her head to soak up and stop the blood from flowing wide. It was to facilitate the sexual attack - he didn't want to get dirty.
I think Guede went to the bathroom primarily to wash hands and rinse his trousers from blood, not to fetch towels. It is of secondary importance if he got the towels from there of it they were already in the room.
I don't think there is evidence of any cleanup of the bathroom floor.