Heya,
Hmm... I have done some "in depth" study of the Raise Dead line of spells in 3.5e, and come to some interesting conclusions - even in the Forgotten Realms, someone able to cast Raise Dead is not easy to come by...
Raise Dead is a 5th level spell, which means that a cleric needs to be at least 9th level to cast the spell. The Priest or the person requiring the Priest to cast the spell must provice 5000gp worth of diamonds
as a spell component that will be consumed in the casting!!!The 5000gp worth of diamonds is not a cost, it's not what the priest charges, it's actually a spell component - think of it as a sacrifice directly offered (and taken) by the god granting the spell.
Now, lets use Baldur's Gate as an example. Baldur's Gate is a metropolis with a population of 42,103 people.
The rules in the 3.5e DMG suggest that at a minimum, the highest level cleric for that sized community would be 13th level, while at maximum, the highest level cleric for that sized community would be 18th level... But because this is such a large community, there are actually four clerics of the highest level. Now, if the highest level clerics were 15th level...
Beneath those four are 8 7th level clerics, 16 4th level clerics, 32 2nd level clerics, and a whopping 64 1st level clerics. So, out of a city with a population of 42,103 people, we can see that there are a grand total of... 4 clerics capable of casting Raise Dead (they are also capable of casting Ressurection, but not True Ressurection)... of course, this is not taking into account any special residents that may also make Baldur's Gate home.
(Of course, if the four highest clerics are 18th level, there'd be 8 9th level clerics, which would mean that there would be 12 clerics in Baldur's Gate capable of casting Raise Dead or better - however, I'm just using static numbers, there could be 1 18th level cleric (2 9th level clerics), 1 16th level (2 8th level clerics), 1 14th level (2 7th level), and 1 13th level (2 6th level) as the highest clerics in the city - for a total of just 6 capable of casting Raise dead of better)
I hope I haven't lost you in all that.

On top of that, you then have Role Playing concerns. How many of those clerics are available to a person off the street? Have the PCs done something that would make that church think positively of them? Are some of those clerics involved in churches that the PCs have offended or are opposed to? What kind of service or cost will the church impose on the PCs who have requested their help? Raising the dead should never be easy.
I can see doing without the monitary cost for raise dead (but not for Gate or Imprisonment). The way I would handle it is that the character comes back with 1 hp, and 1 constitution, and regains constitution at 1 point per day of bedrest. In addition, the cleric must roleplay out the request and give a convincing prayer. The deity also has every right to refuse the request if the raised character is of the wrong alignment or ethos. A badly done request or too many raise dead spells in the same campaign can result in the deity slapping the priest back a few levels or the priest falling out of favor.
A quick look in the Players Handbook reveals that Temporary Ability Damage comes back at a rate of 1 point per full night's rest (8 hours), or 2 points per day (24 hours) of complete bed rest.
Also imposing that penalty goes against the established rules for the spells concerned. Raise Dead has the following penalties: You loose a level, or 2 points of Constitution (permanently) if 1st level. A raised creature has a number of hit points equal to its hit dice (so 1 point if 1 HD or level 1, or 2 points if 2 HD or level 2 etc). Magical diseases and curses are not undone by this process (though normal poisons are neutralised and ordinary diseases are cured). Any missing parts from the body, such as lost limbs, are not restored by this spell. Raise Dead can't bring back to life those who have been made into Undead (even if killed again), or those who were killed by a death effect (such as Finger of Death). Constructs, Elementals, Outsiders, and Undead can't be raised by the spell, and it cannot bring back a creature that has died of old age.
Which is one of the balances on clerical spells that frequently gets lost. High-level clerical spells are requests for aid from the deity. The spell must be cast to aid the ethos of the deity. It is quite possible that Lathander might not want the Lawful-Evil Necromancer in the party to benefit from Heal. An evil deity might prefer to let the Good paladin or ranger die. Mages don't have to worry about being in anyone's favor so they can cast what they want, when they want, and how they want to with impunity.
The philosophy for 3rd Edition is that a numerical benefit (or penalty) cannot be balanced by a role playing penalty (or benefit)... For the game to be fairly balanced, it needs to be based on cold hard rules. Spells work regardless of whom they are being cast on - the god might have a few words to say to their priest later (in the form or a vision or an omen), but I seriously doubt they'd hold back a spell they'd already granted. (That's why priests pray for spells at the same time each day - it's the same as a wizard memorising a spell, which is why clerics don't cast spells like sorcerers.)