Sounds like the issue is two-fold: meta-gaming versus role-playing. If you're meta-gaming, you only need the most efficient option; all other options are moot (sub-optimal). So if a game rewards you for slaughtering your foes more than it rewards for not doing so, then there is only the first option.
And, the other issue is how designers choose to reward players. Sure, in most games, srpgs and blobbers, etc, the goal is to maim and murder everything in your way or win the field at all costs. That's fine, and those games are enjoyable in their own ways, but on the topic of more traditional rpgs, designers really have to come up with other ways to reward gameplay.
Combat can be deep, but any rpg that focuses on it, as the main method of interacting with the world, is going to inherently be shallow in its execution. Of the more interesting systems used, you have Ultima 4 at the top where combat interactions served more of a purpose than just filling an xp bar and your gold pouch. Followed closely by Fallout, and all of its interesting options for obtaining the xps both inside and outside of combat, giving players perfectly legitimate alternatives to combat even in the most critical situations. Unfortunately, after this, things start to fall down fast and hard. You've got KOTOR, and the plethora of other BioWare titles, which ties how you handle npc interactions to a moral system which locks or unlocks certain content and (in the case of KOTOR specifically) certain skills/abilities. And then the vast majority of other games that give you option on HOW to kill and whether you ransack the corpses afterwards or not.
A use-based system and a balanced economy would fix this, but may not be fun. While Arcanum gave experience for every strike struck by your mc, this typically ended in death, ya know, to maximize benefits. In a use-based system, your character would get appropriate rewards for whatever role they filled that particular battle. Eventually, your end-game result is an organic representation of how you play the game instead of some arbitrary abstraction and amalgamation of points. Giving players more mid-combat options such as switching to ranged weapons to pick off fleeing opponents would also be interesting.
Designers could also take the time to make it advantageous to leave enemies alive, as mentioned above, Way of The Samurai has had this since at least the 3rd entry, and Mount & Blade (arguably) encourages using non-lethal combat.
Another option is make combat more lethal. If combat is dangerous as hell, and you can avoid it, intelligently picking and choosing your battles while stealthing past the rest of encounters (ala Thief), then you have something to gain from not being Super Awesome Ultra Guy. A game that does this well, IMO, that I've played is Neo Scavenger. Medical treatment is extremely expensive and, as far as I know, there is only one spot on the world map you can receive it.
So, yeah, kill all enemies is the norm. It's standard. It isn't an adventure anymore, it's a bloodbath. There is no journey, just the trail of corpses you leave between Starter Town and Bad Guy Tower.
