The problem with Raise Dead isn't the spell itself. It's when it's available.
In the days of 1E and 2E, D&D campaigns typically went from level 1 to somewhere around level 9 or 10 at the end. So, Raise Dead was something that was available for the PC cleric to cast only at the very end of the campaign, as you needed to be level 9 to be able to cast it. Heck, you might have only just gotten to level 9 and the campaign is ending, so even if a companion dies, you're at the finale and any Raise Dead would take place after the finale.
And, in keeping with that theme, there were probably not too many NPCs of that level, either. And, you'd need to either convince them to raise your fallen companion, or else make a sizable donation to the church in order to get it done. In short, Raise Dead was generally pretty rare in old D&D.
In 3E, the game was retooled so the typical campaign went from level 1 to level 20 at the end. However, Raise Dead was still something that was available to the PCs at level 9. However, level 9 was now just before the typical campaign got to the halfway point. So, Raise Dead lost its rarity because it was just another mid-level cleric spell. It wasn't special anymore. It's now similar to a wizard casting Fireball in old D&D in terms of level equivalency. However, if you took it out of the game, you're also nerfing the cleric and one of their best mid-level spells.
Then, in 4E, the game was retooled again, and this time the typical campaign was supposed to go from level 1 all the way to level 30 now. However, Raise Dead was made even easier to cast - it was now a level 8 ritual. So, you're not even into the second "tier" of the campaign and you can still bring a PC back from the dead. It's the campaign equivalent of a cleric being able to cast Hold Person in old school D&D - nice, but is it really that special?
So, my thought would be to still allow Raise Dead, but push it back to when it's available to the players. Make it still special and available towards the end of the campaign only - not in the beginning or even in the middle.
To get rid of the deadliness, I'd use something like Revivify, which was from the 3.5E Spell Compendium - you can stabilize a dead companion at -1 hit points if you can cast it within one round of their death before the soul completely departs the body. Edited to add - Revivify means the "dead" but saved PC is still out of the combat, and it also penalizes the group because the cleric has to take his or her turn to cast the Revivify. So, the cleric is not casting Flame Strike to smite his or her foes, he or she is saving a fallen companion who won't be able to help anymore in the combat, anyhow.
Going by 1E to 3.5E guidelines, I'd make Revivify a level 5 spell, as before. Then, have Raise Dead/Slay Living as level 7, Resurrection as level 9 and True Res be an epic level type spell.
