It is a couple of years since we were in Peru but I definitely agree that the Sanctuary Lodge is the only option (if budget permits) in Machu Picchu. Spending the late afternoon in the site as the final buses depart is truly magical. The guards do move you out of the site as it gets towards closing time but trying to be as far as possible from the main entrance when this process starts gives you a wonderful walk through the site almost on your own. We were there in mid August and the buses were mayhem but we didn't suffer quite such bad queues so perhaps we were lucky.
We stayed at Las Casitas Del Colca as part of our trip based on a recommendation from a family friend who had stayed there when it was part of Relais Chateaux and raved about it. It had left R&C and changed management by the time we stayed and the experience was rather underwhelming. It is a spectacular site with around 50 stone casitas on beautiful grounds overlooking the canyon. However, we were almost the only guests making the site eerie, the service was very poor and the food dull. The hotel is set up with its own farm and food gardens but much of it had gone to ruin and there was not much management care of the property. Management may have changed again but I would check recent reviews carefully before booking a trip based on our experience. The hotel certainly has great potential but needs good management,