How do you defeat the Sectopod on Commander Difficulty?

I think you need to shoot it in the back to deal a fair amount of damage

I sent both my squad members to the right of the starting wall and had them shoot at the sectoids. I lifted the walker and ran to the left flank this allow me to shoot at the walkers weak spot on its back

Hope this helps

I managed to defeat it without aiming for the rear vents.

Stay in the area where you start the scene. Pour as much fire into the sectopod's cockpit glass as you can, and use the Recon soldier's Critical Shot and Engineer's Mine powers as often as you can.

Otherwise I had my companions keep the sectoids busy while I concentrated on the sectopod.

As long as your judicious about when you pop up (it helps to have your companions a distance from you so the sectopod can't watch you all at the same time), you can put a healthy amount of damage into it before it flanks you. I emptied a full M14 rifle into it.

Once it does start to flank the stairs, I moved back to take cover against the side walls near the entrance and directed my companions to the other end of the walkway (away from the sectopod). The weird angle means they still get some cover.

At this point the sectopod is so close that the scatter laser is actually viable, and you can pop out and nail it whenever it isn't firing. Once the cockpit glass is broken, the sectoid pilot is extremely vulnerable.