Western Mythology Tropes in Planescape

Maybe use the Archonites from A Tiefling's Exultation and other things on its Codex Caelorum Septem?
http://www.reocities.com/Area51/Vault/9974/codex_c.htm

The problem with encorporating monotheism into the D&D cosmology is that it denies the existence of any other divine beings (Satan is not divine-- at the very best he's equivalent to a quasi-deity, as opposed to God/Allah/etc. who is a greater power, and basically Satan/Shaytan/etc. can only do what God permits him to, meaning that there's zero possibility for Satan to win), it's not cyclical, and there's a predestined 'ultimate end'. Monotheism (aside from some of the less-straight offshoots) also denies the idea of dualism-- that is to say, it denies the ideas such as "good and evil must come to an equilibrium", "good and evil have always existed and always will", and "there cannot be light without darkness". Instead, the existence of evil is more akin to a rift leading to the Far-Realm; it's an inimical derrangement of the cosmos that was never meant to exist.

The Upper Planar celestials are all hypocritical know-it-alls. Paladins exist to burn orc babies at the stake. Nobody can talk about the Church of the Silver Flame in Eberron without, in the same breath, mentioning anti-lycanthropy atrocities or inquisitions, and their clergy consist exclusively of Lawful Evil self-deluders. Sorry to harp on Eberron so much, but they made a new rule for the campaign setting modifying cleric alignments specifically to better facilitate corrupt Silver Flame priests.
That doesn't mean the Church of Silver Flame (as a religion) itself is evil. The writers merely did that to reflect the corrupt clergy/crusader/etc. that mars the monotheist religions IRL.

And then there's the Harmonium. Despite having Lawful Good ideals, Lawful Good members (among other alignments), and a Lawful Good factol, they apparently accomplish nothing but Lawful Evil.
I could be wrong since I never paid much attention to the Harmonium, but chances are they're not supported by the Tome Archons or the paragon angels, nor by the vast majority of their servants. More likely they've been infiltrated by Baatezu disguised as celestials telling them what a great job they're doing and what other things they should do.
The D&D books are quite clear about many types of behaviors that are non-good, so most of the Harmonium mebers who do that stuff would be either Lawful Neutral or Lawful Evil aligned, including PCs. That doesn't mean that it's impossible for a LG PC, even a Paladin, to join them-- in the case of a Paladin, they would simply be unaware of the atrocities, or of the truth value of the rumors thereof.

Is this trope really that chock-full of literary richness to explore or is it just a lot of anti-Vatican animosity that runs deep in the gamer community?
Both, and while the "anti-christian angsttheist" group is quite pervasive (angsttheist being a hypocritical, holier-than-thou, in-your-face atheist-- the atheist equivalent to a 'fundie' or 'bible thumper'-- a pejorative for the arrogant, holier-than-thou, hypocritical, intolerant type who act and think exactly like the group they despise, but get pissed if you tell them that because "I"M NOTHING LIKE THEM BECAUSE I'M ACTUALLY RIGHT!!!!ONE!!) the trope is not limited to just Catholicism analogues. I've encountered plenty of JRPG games with the exact same theme, except in those cases, USUALLY (but not always), there is a young novice priest, monk, etc. who upholds the ideals and decides, in the end, that the ideals are still righteous. It's actually somewhat of a story cliche in that the novice usually works for one of the corrupt head honchos and is mentored by him, and then is forced to confront him later on. In videogames, they're usually forced to kill one another. While most religious groups in JRPGs are modelled after Catholicism, many contain Buddhist elements, and I have encountered one or two games (e.g. Illusion of Gaia) where the corrupt place actually WAS Buddhist. I'm Christian myself, and I've encorporated the exact same theme into some of my stories (although the evil god in these stories is actually an analogue to Satan's "angel of light" aspect rather than "the monotheist god is malevolent and the church is evil" theme you see so often) In all versions of this trope, the major theme is hypocrisy amongst the followers. In many cases there's also an "underdog resistance" theme where some huge, all-encompassing evil empire/church/etc. is brought down by a ragtag group of rebels who are champions of the oppressed little guy.