I guess it struck me because throughout the episodes, he's very careful what he says. He's all about manipulating people and getting everyone into the positions he wants them in. Everything he says has an agenda. But that line is (IMO) straight from the heart. He's not trying to get something from someone, he's not trying to convince someone of something, he's just honestly deeply upset that he killed his old friend.

(Or I suppose you could say that he's faking remorse to get Duncan to feel sympathetic and not kill him, but even I'm not that cynical.)