I wouldn't be overly hung up on this, as the movies and novels parted ways a long time ago, but in the novels he doesn't particularly like killing. He does it if he needs to, but it isn't something that he likes. I think in Goldfinger he is a bit shaken after killing a man. If I recall Fleming refers to it as a Deathwatch beetle on his soul.
Also there was that bit in Casino Royale, during the break in the card game, where he kills three guys. He's visibly shaken and needs a stiff drink afterwards.
But it is entirely open to interpretation. Bond in the Warren Ellis comic is a bit more cold blooded, but is seen as a bit of a maverick by the Service. That's not a bad way to play him for a modern sensibility.