I, too, have mixed feelings about the scene, mixing drama with comedy, of Roger abandoning his son and family with no feeling of remorse. It was truly moving, especially seeing little David standing with tears in the doorway watching him leave. Added to the emotion was seeing Barnabas' reaction which was filled with equal pain and compassion for that child for whom he had become so attached.
At first, I thought we should have seen more interaction between David and Barnabas that would have created that emotional bond between them, but it hit me (duh) that the murder of Barnabas' parents, which drove him mad, already served that purpose.
It helped that while discussing the movie, Nicky pointed out that Roger fits in with Burton's recurring theme of the bad or distant father. Taking that a step further, how often did Burton show the devastating impact of a father's death (
Edward Scissorhands, Big Fish, Sleepy Hollow, Ed Wood [with Bela Lugosi as the imperfect father figure])? And while Barnabas didn't follow his first instinct to kill Roger, he gave him a choice, so it was Roger who ultimately left David without a father, leaving Barnabas essentially blameless.