I did eventually settle on a solution for resurrection and raise dead, in answer to the problems presented in this post. Rather than ban either spell, impose restrictions on their use, impose penalties on the players or any of the other suggestions, I went an entirely different route and lowered the cost of the spells. This was, after all, my actual problem - that players would be able to make hordes of money by sitting on their butts casting their new raise dead spell at 9th level. I did not actually have any problem whatsoever with the presence or benefit of the spell.
While lowering the cost does mean that the players do not need to give an arm and a leg to get raised (which was actually one literal suggestion), the overall availability of raise dead means that unless the party happens to be in a fairly heavily populated area, chances are the spell won't be available. Not because a cleric won't give it, but because there is no cleric of sufficient level around.
Once, when running a party 20 years ago, they found themselves in the Caribbean after numerous adventures, a major character died and there was no civilization at all. Nor was it likely they were going to be returning to Europe any time soon. So the party carefully cleaned up the character's skull of meaty bits, mounted it on a staff and had the cleric carry it around for the next eight months of real time (I was running once/week, so about 30 gaming sessions) before it could be resurrected. They paid heftily, and the player succeeded at his resurrection survival roll. Good times.
Anyway, for me, the problem is solved. A lot of the time the party won't find a cleric in raise dead's time frame, and pay more for the higher spell ... and meanwhile, they themselves won't produce a 16th level cleric for some time.
It occurs to me that a 16th level cleric is such a rare thing in my world that the pressure to use the spell upon only worthy people will be very great. I do impose a rule that you must be of the cleric's religion gain the benefit of certain clerical spells, but not for healing spells: cure light wounds, remove paralysis, remove blindness, dispel magic, cure serious wounds, neutralize poison, raise dead, restoration, heal, resurrection and so on ... any spell, in fact, that does not require the recipient to believe anything. The reverse of all these spells work on non-believers ... why not the good as well?
Where faith matters happens when the spell requires a belief from the recipient. Bless, for example, gives a +1 to hit as a matter of believing the bless has effect. The same goes for chant or prayer. Aid, which is not a healing spell, but the addition of extra hit points, is also a blessing, as is any spell that empowers a recipient. Atonement requires a willingness to believe.
Others might interpret the spells differently, but I'm not concerned with that; this is how I do it in my world.
Where it really makes a difference in day-to-day affairs is the party's paladin. The 10' radius protection, and the lay-on hands, only extends to those who are the same religion as the paladin - i.e., have formally been baptised or otherwise indoctrinated into the religion. And once your player has been, there is a certain responsibility put on the player - cleric and non-cleric alike - in return for that bonus 2 AC (or any other benefit).
(Yes, I do require the same religion for the paladin to heal ... it is a different kind of healing, and does require faith)
Now, it so happens that I am running a mage in my daughter's world, who is about to become 3rd level. I am looking forward to 5th, when I will receive a henchmen - she plays the same rules as me. And it is my plan to roll a cleric.
The party is divided, religiously. The paladin and the druid in the party are Celtic. The fighter, thief and illusionist are Roman Catholic. I am the only undeclared member.
The player who runs the paladin rolled a spectacular character: four 17s. Strength, Constitution, Dexterity and Charisma ... with high rolls for Intelligence and Wisdom besides. He is a formidable powerhouse, and is now moving steadily towards fourth level. If I play the sort of cleric I plan to play, namely an aggressive authoritarian with delusions of divine infallibility, and I pick Roman Catholic, the paladin and my cleric will eventually go toe-to-toe. Which is fine, the cleric only has to endure for two or three rounds for my mage to rip the paladin a new asshole. (of course, he's reading this right now and wondering if he should let my mage live to be 3rd).
Alternately, I could choose to be Celtic. This, I think, could be very interesting, because it provides my character with some immunity regarding the paladin. Gods do not look with great love upon paladins who destroy clerics of their own religion. Kill me, and be a fighter forever.
Of course, this all depends on how thoroughly I play the cleric character. I feel I have a good sense for the dramatic, the screaming of "For Manannan!" as I crush skulls with my mace, the gentle influence of giving alms to hundreds as I enter towns, the patient assassination of hated catholic clerics and the steady anarchy I encourage by converting not the resident humans, but the dispossessed orcs and half-orcs of the nearby hills. After all, Celtic gods are less preachy about racial purity. It might be interesting to have the paladin not as an enemy, but as a puppet, dancing on my string of religious agenda, marching ahead of said wretched denizens of the dark to destroy a hated Gothic church.
Mwah hah hah.
And once again, the paladin is reading this, wondering if I should be allowed to live. But this post is really only written for his benefit. There are things a paladin must contend with, and annoying, pious clerics are the worst.