Um...yes. I just used a storytool, which didn't allow the characters in my group to use clerical magic on their dead parents. There are plenty of spells to dig up all the necessary information (starting with how they died) if their parents' souls had been available.
Here's how I reason resurrection:
A character dies and a intermediary person (an outsider who works for the Deity the character was worshipping) takes him to his rightful place in the afterlife. This can be anything between heaven and hell.
Now, should a person not worship a god his soul isn't taken to the Outer Planes, where the Gods' domains are. Since the soul isn't there resurrection just doesn't work. The spell doesn't find anyone to resurrect.
Should different characters in a group worship different Deities, then there might be a problem as well. A cleric of an evil Deity wouldn't be allowed (by the good Deity) to tamper with the souls in the Good deity's domain (also works the other way around). So, should someone in the group worship an evil deity, then a cleric of a good deity wouldn't be able to resurrect him.
I usually allow clerics of good deities to resurrect anyone who worships a good deity. The reasoning is that Good trusts each other and can allow resurrection of souls by other clerics aside from their own. Evil, however, isn't so trusting. So, you probably won't be seeing evil clerics resurrecting anyone not of their own religion, because Evil deities are much more paranoid and distrustful of each other.