His judgement may have been misguided but the most important thing we learned about the Doctor this week was that he trusts his companion implicitly. Rather than helping Clara -and Lundvik - by explaining the moon would not devastate Earth when the alien hatched, he left them to make the moral choice themselves. It's all part of that ruthless nature we've come to understand and it almost backfires; humanity chooses to kill the alien and save themselves and Lundvik becomes the figurehead of that choice. But Clara too begins to waver and by the point he returns she is frightened and alone and at the point that she too is considering killing the alien to save Earth. Of course Clara presses the button in the end, stopping the bomb from killing the moon, but by then the damage is already done...