Killing or subduing an enemy will result in a loss of points. A loss of points means it takes longer for you to unlock the improved abilities that 47 can gain and making it harder to gain the coveted "Silent Assassin" rating. However, depending on how you perform the kill and take care of the situation, you will gain points back. If executed correctly, you can end up with a net zero point change even after killing someone. For example, if you perform a silent kill (eg. fiber wire with nobody else looking), you will lose a set amount of points for killing someone, but then gain half of it back for doing the silent kill. Then, if you hide the body, you will gain the remaining points that were lost, resulting in no change. This also works for subduing people, then hiding them.
All in all, this method allows you to still earn a "Silent Assassin" rating while still being able to deal with certain people that are directly in your path.
Also, killing or subduing someone will gain you a set amount of instinct, so if you're running low and you depend on instinct, this is a viable way to get more. I'm not sure how instinct works on Purist difficulty.
Edit: It seems that there is no instinct on Purist difficulty, at least in the sense that you can't gain more. On Purist mode, trying to use instinct will only show you where your current target is and slow time down a bit, nothing more. This ability also appears to be unlimited.
Best Answer
You will lose more points if you kill the non-target person as opposed to simply subduing them. As outlined in my answer here, you can gain those points back by not being seen and hiding the body.
If you're wondering about whether or not they will eventually wake up from being knocked out (as in previous Hitman games), I have neither experienced this in-game nor have I seen anyone comment on the fact that they do.