I think it's important to remember that Gygax's game is the dungeon crawler. The game we turned D&D into after Against the Cult of the Reptile Gods and after Dragonlance is not a game whose morality system is intended or designed to tackle global politics or holy wars. It's just meant to tell you which are the monsters you're supposed to kill and which are the people you're supposed to talk to. It's red vs green morality of the sort you find in a video game. The fact that it falls apart when you poke it is not really a valid criticism. It's not intended to endure rigorous Socratic examination.
More than that, I don't think I understand your goals.
Clerics are just as much crusaders and templar knights as paladins, except more so. They don't have any specific origin or inspiration except the Knights Templar. The reason they avoid edged weapons is because some crusaders did. That's where that came from. [Edit: To be clear, this is a myth to the best of my knowledge, but it was a commonly believed myth during Gygax's time and it's what justified this mechanic... it's like ring mail and banded mail.]
Rangers are problematic, too. They're literally forest cops originally centered around the extermination of indigenous humanoids deemed undesirables, and in the context of the Americas are essentially agents of Victorian era colonization.
Monks are David Carradine and Bruce Lee transported to Medieval Europe and still Asian coded.
Barbarians are Conan, but also are indigenous savage tropes from simple brutes to noble savages. Until recently they were illiterate for fluff reasons.
Druids and Bards are caricatures of celtic religion and culture. Warlocks are caricatures of Christian religious oppression. The game freely uses or used terms like shaman, golem, phylactery, djinn, and wendigo.
If you're looking for a game with a problem free use of culture and history, you are looking at the wrong game.