In the game I'm playing in now, I actually sat down with my DM to work out a prestige class for my rogue/cleric. His deity is the god of luck, freedom and trickery (though it's not malicious trickery. More knocking the cruel and the self-righteous down a peg. Tricking or stealing from an innocent is one of the worst sins in their eyes, and fooling a simpleton is like kicking a puppy), so the prestige class is more than a simple merging of clerics and rogues (he gets Knock, Break Enchanment and Freedom as 1/day abilties as levels up) but he also gets some nice synergy, like burning a Turn attempt to sneak attack undead for a round and whatnot.
I just took the second level of the prestige class at the end of the last session, so I don't know if it's going to turn out balanced in the long run, but right now I feel like a crappy rogue mixed with a crappy cleric, though taking Practiced Spellcaster at 6th level helped the crappy cleric part some. Any attempt to turn undead is pretty laughable, though. At least I get "Shank the Unliving" next level so that won't be an issue anymore. I think once I get a few more levels of the PrC under my belt, my character will start hitting his stride, but levels 4 through 7 I was feeling pretty useless. I mostly spent my time playing flank buddy with the real rogue so he could dish out good damage and I could put out passable, and then use my spells to heal people up after the fight. The last fight we were in I did better, but that was because the enemy took a couple rounds to close with us, giving me time to buff myself while waiting for them to get there.
Which I realize doesn't help you with your issue in an official way, hopefully it will give you some ideas of what playing a cleric/rogue is like. I would suggest talking to your DM about putting together a custome PrC for you, or else adapting the Temple Raider class into one that grants cleric spell progression instead of its own list.