In LTK we meet a rather determined and single-minded 007, he wants revenge; his good friend was badly maimed and his wife murdered. Bond feels like he owes them and is driven almost to the point of obsession. There's probably an argument that Bond is in fact the 'villain' in LTK as the line between him and Sanchez is severely blurred. Eventually he is able to kill Sanchez and at the end he seems almost relieved that the man's dead.
Then we go to QOS, where we have a similar situation. Bond's girlfriend has died and the events surrounding her death are rather murky. After finding out that she was being used by Quantum; Bond confronts the man directly involved in the deception but he doesn't kill him, he could, but he chooses not to. Was Bond right to rise above it?
Personally I think it is much more satisfying that Bond lets Yusef live opposed to go on a streak of destruction a la Dalton's Bond. There's a greater degree of complexity on show in Bond's character development. I think a lot of it has to do with Bond's final passing line to Camille: "I don't think the dead care about vengeance", it's a beautiful line. He see's in Camille the hollowness she feels now Medrano's dead. She's hoping that now she will be able to sleep, hoping she will now finally be free. Bond somehow senses the emptiness of it all. I think it's the most important moment in the film It's just a thought that's been in my mind over the last few days and I thought it something maybe interesting to throw out there. Are we happy or should Bond have killed Yusef for what he did to Vesper.
Comments
From a practical point of view that of course makes the most sense, but it is after all a film and I think the thematic thread is likely the most prevalent. M after all seems to have sanctioned the kill or at least turn a blind eye to it. Bond's there to kill Yusef but he decides against it.
Of course the 'Dead don't care about vengeance' speech, and seeing the hollowness in Camille (possibly also the reason he didn't bed her), are a big part of it, but I also see it in a different light: since the beginning of CR we've been seeing Craig Bond become the Bond we know from previous films. But he's been very reckless, killing every lead and all that. That isn't what Bond in the previous films did, Bond could kill, but only when necessary, or when he had no other choice.
So when he walks out of Jusuf's apartment and hasn't killed him, he's a step closer to becoming the Bond we know: he's now learned to show restrained, even when he despises a person to his core, when this person is of interest to MI6.
I think he keeps that restrained until near the end of his career, when a Bond that's tired of doing his job and always following orders goes looking for revenge on Sanchez, Bond's view of the world has now changed, and he has no problems killing Sanchez. (that's if we assume that Craig-Bond will also go/have been on all the other missions, but that's my explanation for why he leaves Jusef alive, but kills Sanchez)