I agree with the OP about taking up a defensive position. The house clearing we did was always based on rapidly building up overwhelming force at critical points. In addition, securing your rear and flanks was a good idea - it's easy to get ambushed. I short, clearing a building is a team sport. Kind of tough if you are the only one on the team.
I also agree with his choice of position. Practically speaking, there is only one avenue of approach to the second floor and that is where his family is. Whether he is at the top of the stairs covering the entrance to the stairwell or back in a room covering the exit is a detail best left to the guy who is going to do it.
His choice of position also distinguishes between what is worthy of using deadly force to protect (people) and what isn't (downstairs property). I agree with that too.
I also like the idea of taking the initiative by letting the burglar(s) know there is someone in the house. I expect that most of them would depart with something they could carry. That's fine by me. If they keep coming knowing the home is occupied, I think it reasonable to fear that they are armed and capable of dealing with opposition.
Finally, while it depends on the weapon, there isn't a whole lot of cover (protection) in a frame house. And my wife would kill me if I put sand bags in her nest.