Mutilation of the body can be fixed. If you can come back from the dead within a minute, you can resume your mission. If the mission was to rescue hostages and they were killed, you can have them raised (or, if they dig being dead and don't want to come back, then maybe it's not so bad to let good people die--hell, feel free to kill them yourself).
There are many logistics involved in it that are also part of the rules, though. Ressurrection isn't a panacea, it's one tool among many. The first and most minor of these is that the returning character will be weakened. In a lot of ways, returning a commoner to life with an 8 Con, condemning them to a slow death from disease and making sure they can't survive a harsh winter, is more cruel than just allowing the soul to die and letting his healthy kids take over. Secondly, and more important for villains, there are several quite mundane ways of death that resurrection cannot thwart. Most necromancy will destroy the soul, either with a death effect or by turning them into undead. Rarer effects will kill them with old age, rendering their body incapable of getting a soul again. You also need the body itself, and there are hundreds of thousands of different ways to end that. You also need 5,000 gp, which is beyond the wealth of any NPC of less than 6th level, or any PC of less than 4th. It is generally a convention in campaign design that NPC's of greater than first, second, or third level are HIGHLY exceptional. This is more true in Eberron than it is in FR, in practice, but the powerful critters in FR are probably better realized as PC's than NPC's. And many books tend to be written about lower-level heroes anyway (definately sub-18th-level).
So in the spell itself and the casting of it, there are many ways to still have tension emerge from someone's demise. A dip in lava. Feeding the prey to a monster. A fall off a cliff. Necromancy. Killing poor people. Stealing a trophy from the body (head-taking becomes an effective measure to prevent resurrection). And any smart villain is going to know the world works this way, and prepare for the eventuality of the occasional resurrection. In fact, he may even work it into his own plan by corrupting or replacing the clerics in town with his own agents.
And intelligent villains who know the way the world works will use those to their advantage. A hostage isn't really a hostage if they can just be raised -- they're a hostage if they are one switch away from an acid bath, to be fed to some great beast, or turned into an undead servant. You can continue your mission in a minute only if the villain doesn't actually threaten you (which requires intelligence and creativity beyond "stick the sharp end into the soft squishy thing"). You can resurrect hostages only if the villain is collossally dumb about takig hostages (again, requiring intelligence and creativity), and if the hero is for some reason fantastically wealthy (which, admittedly, many high-level characters are).
People have been using these in their games for years, now. Why do the novels have to work around it? The only answer I can think of is that the authors don't want to deal with the challenge of writing in the game world. They want to tell their pet story, and rules of the setting be damned! Instead of using their creativity to deal with the problem of resurrection as any intelligent villain in that setting would deal with that problem, they fold over and ignore it. And for my tastes, that's just BAD writing, at least from a game-novel perspective.
There is lofty, high-handed thematic tension that you're talking about, but there is also the very palpable tension of a character being one false move away from death. Apparently, you're arguing that the lofty, high-handed thematic tension should completely supplant the tension provided by a cool action scene or a tense battle to the death. Guess that's your personal taste, but it tastes pretty watered-down to me.
Just because resurrection is a factor doesn't mean that the character isn't one false move away from death. It just means the villains have to be written smarter than "poke it 'till it stops moving." At the most orcish-intelligence level, it's "poke it 'till it stops moving, and if it looks fancy, cut off it's head and take it back with you. Also, make sure that the most powerful preist in the world doesn't have a thing for it." This adds flavor and dimension to the world, heightens verisimilitude, and embraces the game that the setting is supposedly set within the rules of. It makes the heroes have to thwart the plans of people in a fantasy world. ANY book can be written about one-false-move-away-from-death. They are. Every day. Only in Fantasy can you even ponder the nature of "one-false-move-away-from-undeath," or the like. And more specifically, only in a fantasy game would the idea of fairly common resurrection even enter into it.
Furthermore, characters don't need to be one step away from death to be one step away from destruction. Death is just one kind of destruction, and, IMHO, an over-used dramatic schmaltz to wring tension from a situation. Death in the usual literary sense is final, irrevocable, and unsympathetic. This is why it's a useful shorthand for the destruction you want to scare the main character with. Death is death, but TRAGEDY is drama. The fact that writing a novelisation for an RPG limits the ways in which you can use death as a shortcut is one of the things that makes it an RPG book, a fantasy book, and no other kind of book.
Milton didn't need death to make drama in the garden of Eden. Dante didn't need death to introduce tension to his spirit-quest. Homer told you what was going to hapen before it ever happened, so death was always an expected consequence when it happened (Achilles), or there was no fear of it (Odysseus). Hercules didn't fear demise in his 12 labors. These are epic and legendary adventures, and any hero that can bring people back from the dead, call fire from his fingertips, slay three men in six seconds, enchant swords, or hide from the gaze of celestials and pick the locks of the world bank is automatically in their league. Largely, D&D novels are like D&D games: stories about the exceptional and grand individuals that are surrounded by seas of the weak and innocent (e.g.: the audience). The ability to control life and death is one aspect of this magnificent power, and as such it should not be dismissed and hand-waved, but embraced and confronted. Everyone knew Odysseus was immune to death and that he'd get home eventually. The story isn't about his potential failure. It's about the adventure.
