I was thinking about this too. Usually when I experience PCs refusing to run from a fight it's really simple. TO them, Fight = Reward. Not even going into the possibility of treasure, usually the reward in question is simply Exp.
My hypothetical solution to this? Don't grant the exp biased on individual encounters but rather just in bulk all at once once they reach the appropriate point to level up. (Or even alternatively opt out of giving exp all together and just inform them once they hit another level).
This really would be a tactic you would have to run by your players first though as you would want them to be clear on what's going on. Last thing you would want is for your players to think they weren't getting any opportunity to advance
But yeah, take out the reward and hopefully your players will realize that there's no real gain to fighting everything they come across.
Unfortunately this doesn't solve the kinds of characters that just simply want to fight for the sake of fighting and/or honor. In those cases? Yeah... you probably will have to start killing people off to get your point across as everyone else has mention...