Siempre Viajando has pretty much summed it up. Flights are easy and LAN is a good carrier. 3 days two nights would be the minimum. You can book tours at the airport there are a few tour companies there and they seem like good value.

If I was you I would add an extra day to acclimatise and maybe a trip to the Sacred Valley.
Day1- Fly into Cuzco transfer to hotel and walk around city
Day2- Tour of Sacred Valley
Day3- Train to MP, day in MP and train back to Cuzco
Day4- Fly back to Lima