It's no secret that Felltower is a meatgrinder. It's a tough megadungeon, it gets more and more lethal as you delve deeper, and all too often PCs have delved too deeply or chosen poorly while doing so and suffered casualties for it.
The fatality rate of clerics - and acolytes - has been especially so. From Inquisitor Marco early on to Felix Aurelius most recently, clerics and acolytes have rarely survived long in Felltower.
Here are what I think are some possible reasons.
Acolytes aren't full-fledged delvers. Let's just get that out of the way right way. An acolyte is a 125-point character. Felltower is routinely lethal to 250 point characters. So NPC "clerics" hired or brought on as Allies are likely to die much more quickly when bad things happen. They can't survive as much as a cleric can.
This has spelled doom for all of the acolytes - eventually, they get into combat and die, or caught in an area effect and die, or breathe something and die, etc.
Inherent weakness of the cleric template to damage. Clerics have only ST 12, and HP 12, and HT 12, to start with. That limits their ability to rack up a lot of high-DR armor or take punishment that's routine for knights and barbarians (HP 14 and 22, respectively, and both are usually higher - HP 20 is all but standard on knights in my game.) They end up slow (lower Move, lower Dodge), relatively fragile, and
People think of wizards are fragile - and they are, once you actually can hit them. They don't have as low of a Dodge score, add a shield and their defenses are pretty good, and it's unusual to have a wizard without an effective broad-use Blocking spell like Phase or Blink. They're at first glance more vulnerable than clerics but in practical terms they're harder to just clip with a good attack and take out of the fight.
A number of clerics have died because they just couldn't handle a single hit.
They aren't backup fighters. Clerics start with a 14 or 15 in weapon skills. This is just enough to get in the door as a potential combatant. But fodder monsters often have skill 14-15 - even the "attack in swarms and die in batches" dinomen have 14s. ST is 12, which is good for 1d damage. They can't do much more than usually hit and maybe cause damage. With ST 12 and a mace (sw+3) damage is 1d+5. That's 6-11 damage, average 8.5. A broadsword would be 1d+3 - 4-9, average 6.5). That means 2-3 blows in most cases to take out a HP 12, DR 3-4 foe. Compare this to, say, a Knight with skill 18+, ST 14 (so 2d+1 with that sword, doing 3-13 av. 8) without even dipping into more ST, Weapon Master (both are common), and who may have higher skill and Extra Attack.
In a pinch, yes, a cleric can fight. But they don't do it well. Buff spells and Heroic Feats (allowed in DF, not in DFRPG for what it's worth) are a good way to briefly allow a cleric to bring himself up to fighting spec . . . but they rely on time, random rolls (for effect or to cast), last a brief time, and cost points that draw away from other priestly roles. They're probably better for emergencies than for making your cleric into a combatant.
They just lack the skill, ST, DX, and HT of a front-line fighter, plus lack the special abilities (Extra Attack, Weapon Master, Trained By A Master, Enhanced Defenses, Combat Reflexes) that augment and multiply the effect of those stats.
I think D&D and AD&D rather permanently ingrained the idea of the "fighting cleric" or of the cleric as a "get in there and mix it up" class. You're a cleric, you cast some healing here or there, smite some things with your holy powers, and turn undead - and when you're not doing those everyone should fear your mace or hammer.
In GURPS Dungeon Fantasy, you can do all that . . . if you're around 400 points. And you won't do the fighting nearly as well as a 250-point dedicated fighter-type. You just won't.
In Felltower, this "not a backup fighter" reality has clashed with "clerics mix it up with Evil!" feeling. In our very first play of DF, playtesting Mirror of the Fire Demon, a cleric was killed by an ogre when he thought he was good enough for front-line combat. The clerics who have fought have found that their contribution is helpful but relatively paltry, or that they can't hang and die. Sometimes both.
I think those are some of the reasons why clerics, especially, have ended up dead all over the place in Felltower.