I think you are misunderstanding the house layout though.I thought that maybe if the killer left closer to dawn, so the blood was still thin, or perhaps he was bleeding. Then Haruko when she came in the morning could have stepped into the blood. It looks like a small shoe. It appears somewhere mid-way, so maybe this is where she stepped into that pool.
Could it have been that he left closer to Haruko coming in?
Or, could he have left between Haruko buzzing, then coming back to retrieve the keys and returning back? It could explain the discrepancy between the fact that the first time she came, the door was locked (killer inside) and the second one, open (opened the door and got out). If she entered the house and saw/smelled it, she could have kept the shoes on.
I highly doubt it's Haruko's: the picture of the alleged sock footprint Incoherent posted is at the second floor. Even ignoring the grim possibility that Haruko jumped over Mikio's body, the one sock footprint would really be the only trace she would leave?
We also have a picture of the entrance and there are no other footprints like that (and also, in the documentary you can see shoes' footprints going TOWARDS the front door, while there are no traces going inside the house FROM the front door.)