my guess is that Gus wants to ruffle Walt's ego. by giving him half the dough for Jesse's meth, Walt is now linked to the "inferior" meth -- we know how much Walt prides himself in cooking the purest meth, so this will probably just push Walt into cooking again.
i always thought that the show started off as black comedy. comedy obviously took a backseat in the second season when shit got heavy. they're slowly injecting back the humor (pizza on the roof, for instance). i like how it straddles both comedy and drama now.