Yeah, this is one of those areas in the design where the meta game gets lathered over the imaginary world.
Basically the issue is that the system assumes that to defeat someone you have to either chew away their hit points, or they fail a saving throw. This goes back to the very beginning of D&D where the hit point system was invented so that there would be a cinematic pacing mechanism to make combat stretch out long enough that it would be interesting. Back in the day the inspiration pointed to would be sword fights in Erol Flynn movies. People don't get cut down in one shot usually, instead you've got several minutes of swordplay to build up the drama and then finally the bad guy gets nailed in the end.
Despite what the rulebook defines hit points to be, they were and continue to be a narrative construct. It gives the mechanics breathing room for a story to emerge in the action.
The problem with cliffs is that it's more like a save-or-die effect. It's an either/or condition and if its sufficiently high or over lava then you die. So if you can knock someone off the cliff then it can bypass the hit point system. Normally save-or-die effects are something that is well regulated on when they can be used. You have to have a spell, which can only come at a certain level, and is a resource that is used up. Thus, the system regulates when these can happen and they can't be spammed.
This is one of the inherent problems with D&D is that it gives mixed messages. At it's heart is a narrative pacing system so that fights feel more like a movie scene. However there is also a lot of stuff that dangles a sense of simulation. There are rules for all sorts of things that tie into what one could see as a physics engine. That simulation and narrative elements can clash sometimes.
What it comes down to is that the system wants to avoid having a BBEG die on the first round of combat because they got knocked off a cliff. A fight is supposed to be three to five rounds of exchanges and THEN the BBEG can go down.
There are many ways to solve this. In 4e they instituted the bloodied condition where certain things only kick into effect once someone is below 50% of their hit points. A 4e solution might be to have a power like the punishing kick feat, where you can knock someone back, but they have to land in a safe spot unless they are bloodied, at which point they can get tossed into whatever place happens to be there.
Fantasycraft is also more observant of the narrative framework of the game. They have opponents tagged as either mooks or "named" bad guys. Things affect these opponents in different ways, with the named bad guys having a lot more durability to increase the chance that the dramatic arc of a fight can be achieved. It's fine to knock Stormtroopers off of bridges all day if you like, but to take out the Emperor means dialogue and Vader picking him up and getting friend in the process. When Indy shoots the swordsman in Raiders, it's framed as a joke, because there was this expectation for a big fight, but it was the fact that it was an exceptional contrast to how the fights normally work (such as the brawl on the truck) that made that funny. If the whole movie was realistic and grim one-shotting then it wouldn't have been a high adventure film.
In terms of PF solutions. One of them is just to handwave the safe zone rule away. How often people are going to be on the edge of a cliff is mostly in the control of the GM. If they don't want a BBEG to die that easily, then don't have a fight up high or close to a lava pit.
Another solution is to use Hero Points and use them as a narrative currency to let people accelerate the narrative by spending those points. If a player wants to one-shot the BBEG before he monologues, that's fine but they have to pay for it. They are trading dramatic resolution with expediency, which later on my cost them when they don't have the Hero Points available to save the character from the grim expediency of a different BBEG.