So...just to get this straight. We can choose to not carry out missions (like choosing not to kill someone) but still get 100% completion, right?
Actually, Niko doesn't have to do everything that is asked of him. On several occasions as you play through his story, you'll be presented with decisions that afford you the option of doing what you think is right rather than blindly following instructions. You don't necessarily have to kill a target if he or she promises to disappear, but you have to weigh the risk of your employer finding out against the possibility that the person whose life you spare might prove useful later in the game, or even have work for you in the form of bonus missions.