This really does break my heart, cause you tend to forget that the Doctor was a dad once. And then you realized that he had a wife and kids, and he destroyed Gallifrey. Doctor Who punctures your heart, people.
But remember the Doctor's face in this scene. He is not overjoyed at the reunion. He is shocked at what his companions have become. Martha Jones, willing to destroy her race to save the Universe, just like the Doctor. And Rose Tyler, cheering it on.