Dumbledore is an old man who has learned to be cold through years of pain. Alastor Moody is an old man who has learned to be paranoid through years of conflict.

Harry Potter is a young boy whose "unique genius," as Dumbledore put it, is in creativity that is willing to consider evil. Dumbledore's hope was that Harry would behave as Dumbledore and Moody do, without having needing to live through their pain and conflict, simply because he could imagine what would happen if he were soft when he needed to be hard. And so when Harry behaves as Dumbledore and Moody wouldn't, Dumbledore's reaction is "if you had lived through the pain and conflict we have, you would behave like we do." The implication is that Harry has not lived through enough pain.

D's reaction to H's "my parents are dead" speech, specifically the phrase about H's innocence, matches what I would expect if D looked at the 11 year old boy in front of him and saw an 11 year old boy, not someone who had spent long nights contemplating that he was an orphan. When H reveals how much hurt he carries, D realizes that his approach was mistaken, and apologizes.

An alternative interpretation is that D's surprise and apology were because he didn't know H had the memory of H's parents' death, and thought that because of H's adoptive parents he didn't consider himself an orphan / didn't have much hurt there. That is, D remembered that H's parents were dead, but didn't realize how important that fact was. It's a possible interpretation but I prefer the first.

[edit] It is unclear to me, though, why D doesn't use the Pensieve to teach Harry about Voldemort, Riddle, or his parents. If the boy lacks in experience, and you have a magical experience transference device, the solution should be obvious.