Not allowing godless clerics can be a campaign descision, and I've got no beef with it. If Gods -> Matter -> Creatures, and that's why they worship them, and godless clerics are like "WTF?!", okay. That's no more a drastic campaign decision than outlawing Paladins, or allowing Shugenja. It's just part of how you define your world (though I still think it's misguided, but meh). A philosophy can easily be reprsented by a deity...you pledge yourself to Goodness and Protection, and there's a god for it. You pledge yourself to Evil and Destruction, and there's a god for it. You pledge yourself for Enlightenment and Self-Awareness, there's a god for it. I can live with that.
I have a LOT of trouble accepting that the very concept of a godless cleric is stupid, munchy, and nonsensical. It isn't. There doesn't have to be some dude in the clouds allowing the clerics to cast spells. To assume there must be is not only narrowminded, but also a house rule.
WHY DOES THERE HAVE TO BE A DEITY?!
I can understand if that's not your personal preference, or if you don't allow it in your campaign. However, I can see no reason to think that there has to be one, or it's arcane, and there's no reason to think that things are somehow redefined because of that...how is a philosophy more nebulous than "some guy in the sun"? Or even more nebulous than Arcane magic, which doesn't even HAVE a source according to the SRD...the only 'source' for arcane magic is mentioned in that every bard spell has a verbal component...how is that more nebulous than adherence to a philosophy?
According to the SRD:
Unlike arcane spells, divine spells draw power from a divine source. Clerics gain spell power from deities or from divine forces. The divine force of nature powers druid and ranger spells. The divine forces of law and good power paladin spells. Divine spells tend to focus on healing and protection and are less flashy, destructive, and disruptive than arcane spells.
See divine forces? It's wonderfully open-ended...philosophies could be divine forces...Nature is called a divine force...the Moon could be a divine force...hell, by the rules, Paladins are *nessecarily* godless (instead gaining power from Law and Good), and don't need to appease any deity.
How does that mean we have to re-define divine magic?
Arcane magic, meanwhile, doesn't even specify a source, hinting that you could even cast arcane magic from a deity or divine force...imagine that....a Sorcerer could be a 'clergy member' in any world, and *actually* gain *real* spells from the deities.
It's also weird that those who have trouble with godless clerics have no trouble with pantheon-worshipping clerics, which is in effect ALMOST like allowing a cleric to choose any two domains ANYWAY....why do you have to have a pantheon?
There's no real balance issues (otherwise it wouldn't've made it through the intense playtesting of the Core Rules, and there'd be more advice in picking domains for new dieties than 'whatever fits'). There's absolutely no definition issues. Thus there is only the issue of personal preference...which is all well and good as far as it goes, but then you have to allow others to have equally as valid, if differing, personal preferences, no?