I think 4e makes what you did more legitimate within the rules, because 4e is much more upfront that the action resolution mechanics aren't a total model of the gameworld's causal processes, but rather a device for resolving the particular conflicts in which the players, via their PCs, are invested.
Not only does this make it clearer (in my view) that there can be a wound that can't be healed simply by restoring hit points (it's just that no PC ever suffers such wounds when they fight, for narrative/plot-protection type reasons).
So an PC's interaction with an NPC isn't a "particular conflict in which the player, via their PCs, are invested"?
This I think strains credibility, and as a player, I would like to think that I could become invested via my PC in an NPC. One of the foremost jobs of the GM is creating memorable NPCs that you can invest emotion in, much as you could with the characters of a good novel. Indeed, the whole point of the orginal scenario seems to have been to encourage the players to invest in the interaction with the NPC. Which is why I find the fiat scene resolution to be so counterproductive. 'Cut scenes' in which you can't effect the outcome even though my character concievably has the ability to do so are jarring even in cRPGs where I have reduced expectations of player freedom.
It's one thing to have an argument about scene framing and say, "Well, for the purposes of scene framing, a DM doesn't have to play out the scene. He can simply construct the scene by fiat - the destroyed fort for example - without doing the game mechanics resolution - he doesn't have to run the battle or establish the army size from precise calculations of the regions demographics. A DM doesn't have to exactly prove that the band of Hill Giants can find enough food in the arid badlands to survive. A DM only has to make these events and decisions plausible, so that the players don't have suspension of disbelief harmed by finding 8 hill giants living behind a sealed door in a 30'x30' room deep in a dungeon down a 5' wide corridor with no apparant means of egress or physical support.
But for the purposes of scene resolution, then I think that players have a reasonable expectation that everything that they interact with will obey some sort of knowable rule, even if only 'common sense'. If a character can't be healed by normal magical means, then it ought to be obvious why and make sense within the context of the game. For example, if I was really compelled to make it clear that the poor schmuck couldn't be healed I probably would have run the scene as follows:
"In the center of the courtyard, you find a ring of crosses, about which have been piled the mutilated bodies of many of the forts defenders. Here, the few survivors were apparantly tortured to death for the amusement of the victors. The bodies on the crosses are horribly mangled, with severed limbs and broken legs. A murder of crows picking over the dead. Agitated by your arrival, some flit cawing to the eaves of the burned out buildings and stare at you curiously. Just at this moment, you here an agonized moan from one of the bodies on the crosses. One of the figures is apparantly still alive... Although his eyes are missing, you are able to recognize the Captain. It seems impossible that he is still alive. His torso has been split open, and its clear that several major organs have been removed. A glowing green rod has been thrust through his chest, but as you approach he seems to hear you and cries, "Who is there. Help me! Kill me!".
In my game, the above scene would probably provoke at least two Horror checks from the party. I would think that also the above scene gives enough clues that the Captain is not in a state where 'Cure Light Wounds' is going to be of much help.
One that was established, then if the PC's had the resources to heal the NPC, fine. Granted, the problem with the above scene is that it requires that the NPC's have significant necromantic resources to have actually set that scene up. It's not something an ordinary war band of goblins is going to be capable of. And granted, you are going to have to be careful about the mechanics of something that is apparantly preventing death regardless of the state of the character, but as a matter of achieving the immediately desired result I find the above scene framing far better than, "No, you can't just cast Cure Moderate Wounds because I say so, and if you don't like it then just go home."
I think it also makes it easier for the GM to engage in more obvious scene-framing - whereas in a mechanics-as-physics model, there is more pressure to extrapolate each new scene from the previous one by an applicaiton (actual, or hypothetical) of the mechanics, which makes introducing options for which the mechanics don't allow more tricky.
Once the PC's are interacting with the environment, you've gone beyond scene framing.
RM can so easily bog down because there is no way for the GM to "switch off" the action resolution mechanics without creating the risk of deprotagonising the players - because the consequences of the mechanics are all-pervading and total, rather than confined to PC-focused conflicts in the manner of 4e's mechanics.
You've not convinced me that you've avoided deprotagonizing the players. You'll have to demonstrate that trying to heal an NPC wasn't a conflict focused on the PC's, and that if it wasn't a conflict focused on the PC's that you've still managed to protagonize the players in the scene.
To me, the preference for that sort of approach seems to follow from a mechanics-as-physics orientation, which then makes it hard (without "cheating") to introduce a wound that can't be inflicted on a PC via the action resolution mechanics.
DMs are effectively all powerful. If you are ever feeling uncomfortably constrained as a DM, you aren't really understanding the wealth of options available to you. That isn't to say that you shouldn't constrain and limit your own authority, but I don't think there is ever a time when a DM shouldn't feel as if he has enough authority. You can always create something. For example, magic items, like the one implied in the above scene framing, are a very easy way in D&D to introduce whatever rules exceptions you desire.
Actually crafting the house rules you need is another way.
I haven't played much 3E, in part because (i) it seems to support the mechanics-as-physics approach, but (ii) it uses a hit point mechanic that I think can't be reconciled with that approach (for the reasons I've given upthread) and therefore (iii) tends towards incoherence in its approach to damage. Given that fighting and damage are such big parts of mainstream fantasy RPGing, this tendency towards incoherence is a deal-breaker for me.
Odd, but I find 4e far more incoherent. Which just goes to show that the DM is more important than the system. I'm willing to believe that your 3e game would be incoherent. I equally believe that I'm unable to DM 4e in a coherent fashion. I think I can manage with 3e though.