I think there is a sort of conditioning by negative reinforcement here. (Or is it punishment, I always get those mixed up).
If the players learn that leaving NPCs or Monsters alive means facing them in combat again (with greater resources) then they will not do it.
If they learn that running away means getting chased, or giving the bad guys a chance to heal up, they might not.
The question remains how to (in a sensible fashion) get combats to be resolved in the players favor doing both of those things.
Here are some crazy ideas...
1. (Vanquish) Character who make a successful diplomacy or intimidate check. (There will be some correlation between their level of health, your HD compared to their etc..) If you succeed your opponent is made into temporary henchmen. Healing, feeding and otherwsie taking care of them may convert them into permanent ones. This would definitely make it in your interest to give them a chance to surrender and join you. It would almost always be superior to simply killing them, since you get both the xp for defeating them, and their help against the next opponent. Even if you fail, it will give the opponents an opportunity to flee if they can.
2. (Morale Checks) Whenever combat begins, for each critical hit, and at the death of any team mate, roll a will save for the combatants (based on the CR of the opponents DC=10+/- the difference in CR). If they fail, then they are shaken, the second occasion makes them frightened. If the opponent gets shaken or firghtened, then they move up on the scale. Now this might force people to back off, and force them to roleplay the situation. Some players may reject to this, they like to think morale is only an NPC thing (that could work as well).
3. (Surrender or truce) If the bad guys offer reasonable terms of surrender or truce, and stick to them, the players might also do that. Using AU's rules for Oaths and such things can expedite such solutions.
4. (Mercy Points) Like Hero points or Action Points. A player can grant mercy (life, escape, capture, etc..) to a fallen foe. This gives the player a 'ercy point' which they can then play whenever they need it. So day one the party encounters a troop of orcs, and easily brings most of them to neg hps, they show mercy and heal them up to a couple hps each and tells them to get out of the king's wood. This gives them a 'mercy point'. Day three they run afoul of an nasty troll, he knocks the cleric to negative hps... The play the mercy card and ask the troll if they can retreat to take care of their priest. The troll fearing the human gods, allows them to retreat but promises no such mercy later. These would have to be played in appropriate ways in the game and not abused, just like hero points or action points. But they could work.
Anyway there are some ideas.