Correct me if I am wrong, you are suggesting that the window was either intentionally or accidentally broken that night and that John swept up the glass because he wanted to make it look like an "inside job" (i.e. someone who had a key). Its an interesting theory, but I don't see the reasoning behind why John would want to narrow down the list of suspects to a chosen few? Why not leave the glass and make it look like a random intruder? A lot more suspects that way.
If you are going to disbelieve John's forgotten key story, I would suggest that it happened differently. Perhaps Burke hits her, then breaks the window to suggest that someone came in to the basement and killed her? But he broke the window from the inside and most of the glass went outside, so that necessitates a cleanup. It would also possibly explain how the flashlight came in to play, John needed it to see all the glass outside.
Something along those lines, yes. As you suggest, the window may have been broken from inside (So accidentally, or without thinking it through) necessitating a cleanup and making it impossible to use it as an intruder entry point. John may not have wanted to narrow the list, but what choice did he have if the window couldn't serve as the entry point? They had to have a story to explain the break, and at that point it had to become an inside job. Why not leave the glass and make it look like a random intruder? Exactly my question. They may have had what could serve as a rational explanation for how someone got into the house, so why "unstage" it, as per Doc's theory then try to make it an "inside" job ?
One more possibility is that it was broken from "outside" (e.g. the window was swung into the basement and the pane hit from the outside but they feared the pattern of glass on the floor was not convincing -ending up in the same place as your inside break idea.