The companion is the one who is supposed to remind him where the line is, to pull him back from it. Now we have Clara really understanding the Doctor, knowing what it’s like to be him even for a short time. She’s making the hard choices and that unbalances the Doctor. He’s left sitting there wondering what he’s done to this lovely woman. What Davros said in the S4 finale is very accurate. The Doctor ends up turning his companions into weapons