You can't really take points away from a wisecracking protagonist if they crack wise after murdering someone... because that's part of what you do in a game, or read about in comics, or see in movies. Jak & Daxter, Ratchet & clank, Spider-Man, John McClane, and even Batman (sometimes) all crack wise after, or shortly before, murdering someone. And those are just off the top of my head.
And it's been a while since I played Uncharted 1 or 2, but I'm pretty sure he had other motivations. It might've been his initial motivation (you know, because he's a treasure hunter), but if someone saves the world, can ya really call them a douchebag just because their initial intentions were to steal something? People change, and that makes Drake all the more believable.
Seems to me like you're grasping at straws for reasons to hate him, but to each their own.
Oh, and sorry for going off topic...