The 20th century and 21st centuries have been the only times there have been true godless clerics. You can see them competing with Justices of the Peace to see who can perform the cheapest marriage ceremonies and funerals. If people want to use magic that doesn't involve gods, they can become arcane spellcasters and manipulate magical forces scientifically or because of a natural affinity.
I have to say, I don't care how long godless clerics have been around, they are another aspect of D&D trying to run a medieval world based on modern values and ideas with armies that have precisely 50% female soldiers.
If people want to create a spellcaster class that can wear heavy armour, good for them -- just don't call them clerics and change the spell list so things like "miracle" aren't around. Clerics are religious officials -- period.
In some worlds, I base clerics' powers on a link with an objectively real divine entity that acts through the cleric. In some, I base clerics on the idea that religious observances and rituals draw magical power out of worshippers and place it in the hands of clerics; Runequest was an excellent hybrid of these two ideas. The point is that power flows through the cleric not from the cleric, thus the different magical mechanic.
These two approaches allow for just about any sort of religious official, regardless of the philosophy. A godless cleric is a bad way to go not because of the doctrinal problems that arise but because of the liturgical problems. I don't care if the cleric is part of an organized religion or disorganized movement worshipping a single god, a set of gods or the god of a monotheistic pantheon -- what makes a cleric a cleric is his involvement in a ritualized enterprise that involves a collective -- even if he's out on the frontier surrounded by heathens, he is still connected to that collective enterprise.
My view is that a magic system that is based on the inherent power in an individual rather than one which either manipulates natural physics (Wizards) or draws power from forces external to the person (Clerics, Rangers, Paladins and Druids) is already well-covered by the Sorceror and Bard classes. If people want to go further with that idea and create different and new classes of this ilk that are based on a person's moral uprightness attunement with the universe (Wisdom) rather than raw presence (Charisma), such a character would probably more closely resemble the monk than the cleric.
The point is that if people want a heavily armoured spellcaster, they should make their own class rather than piggybacking this idea onto a class that has a an existing set of generic associations.
Remember my point about level dependent abilities.
